1
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Kang RB, Li Y, Rosselot C, Zhang T, Siddiq M, Rajbhandari P, Stewart AF, Scott DK, Garcia-Ocana A, Lu G. Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles. Genome Med 2023; 15:30. [PMID: 37127706 PMCID: PMC10150516 DOI: 10.1186/s13073-023-01179-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/12/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) provides valuable insights into human islet cell types and their corresponding stable gene expression profiles. However, this approach requires cell dissociation that complicates its utility in vivo. On the other hand, single-nucleus RNA sequencing (snRNA-seq) has compatibility with frozen samples, elimination of dissociation-induced transcriptional stress responses, and affords enhanced information from intronic sequences that can be leveraged to identify pre-mRNA transcripts. METHODS We obtained nuclear preparations from fresh human islet cells and generated snRNA-seq datasets. We compared these datasets to scRNA-seq output obtained from human islet cells from the same donor. We employed snRNA-seq to obtain the transcriptomic profile of human islets engrafted in immunodeficient mice. In both analyses, we included the intronic reads in the snRNA-seq data with the GRCh38-2020-A library. RESULTS First, snRNA-seq analysis shows that the top four differentially and selectively expressed genes in human islet endocrine cells in vitro and in vivo are not the canonical genes but a new set of non-canonical gene markers including ZNF385D, TRPM3, LRFN2, PLUT (β-cells); PTPRT, FAP, PDK4, LOXL4 (α-cells); LRFN5, ADARB2, ERBB4, KCNT2 (δ-cells); and CACNA2D3, THSD7A, CNTNAP5, RBFOX3 (γ-cells). Second, by integrating information from scRNA-seq and snRNA-seq of human islet cells, we distinguish three β-cell sub-clusters: an INS pre-mRNA cluster (β3), an intermediate INS mRNA cluster (β2), and an INS mRNA-rich cluster (β1). These display distinct gene expression patterns representing different biological dynamic states both in vitro and in vivo. Interestingly, the INS mRNA-rich cluster (β1) becomes the predominant sub-cluster in vivo. CONCLUSIONS In summary, snRNA-seq and pre-mRNA analysis of human islet cells can accurately identify human islet cell populations, subpopulations, and their dynamic transcriptome profile in vivo.
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Affiliation(s)
- Randy B Kang
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Present address: Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Yansui Li
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carolina Rosselot
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Mustafa Siddiq
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Prashant Rajbhandari
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew F Stewart
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Donald K Scott
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adolfo Garcia-Ocana
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Present address: Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Geming Lu
- Diabetes, Obesity and Metabolism Institute, and Division of Endocrinology, Diabetes and Bone Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Present address: Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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2
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Church JA, Grigorenko EL, Fletcher JM. The Role of Neural and Genetic Processes in Learning to Read and Specific Reading Disabilities: Implications for Instruction. Read Res Q 2023; 58:203-219. [PMID: 37456924 PMCID: PMC10348696 DOI: 10.1002/rrq.439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 06/29/2021] [Indexed: 07/18/2023]
Abstract
To learn to read, the brain must repurpose neural systems for oral language and visual processing to mediate written language. We begin with a description of computational models for how alphabetic written language is processed. Next, we explain the roles of a dorsal sublexical system in the brain that relates print and speech, a ventral lexical system that develops the visual expertise for rapid orthographic processing at the word level, and the role of cognitive control networks that regulate attentional processes as children read. We then use studies of children, adult illiterates learning to read, and studies of poor readers involved in intervention, to demonstrate the plasticity of these neural networks in development and in relation to instruction. We provide a brief overview of the rapid increase in the field's understanding and technology for assessing genetic influence on reading. Family studies of twins have shown that reading skills are heritable, and molecular genetic studies have identified numerous regions of the genome that may harbor candidate genes for the heritability of reading. In selected families, reading impairment has been associated with major genetic effects, despite individual gene contributions across the broader population that appear to be small. Neural and genetic studies do not prescribe how children should be taught to read, but these studies have underscored the critical role of early intervention and ongoing support. These studies also have highlighted how structured instruction that facilitates access to the sublexical components of words is a critical part of training the brain to read.
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Affiliation(s)
| | - Elena L Grigorenko
- University of Houston, Texas, USA; Baylor College of Medicine, Houston, Texas, USA; and St. Petersburg State University, Russia
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3
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Wang Z, Zhao S, Zhang L, Yang Q, Cheng C, Ding N, Zhu Z, Shu H, Liu C, Zhao J. A genome-wide association study identifies a new variant associated with word reading fluency in Chinese children. Genes Brain Behav 2023; 22:e12833. [PMID: 36514817 PMCID: PMC9994172 DOI: 10.1111/gbb.12833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 11/20/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022]
Abstract
Reading disability exhibited defects in different cognitive domains, including word reading fluency, word reading accuracy, phonological awareness, rapid automatized naming and morphological awareness. To identify the genetic basis of Chinese reading disability, we conducted a genome-wide association study (GWAS) of the cognitive traits related to Chinese reading disability in 2284 unrelated Chinese children. Among the traits analyzed in the present GWAS, we detected one genome-wide significant association (p < 5 × 10-8 ) on word reading fluency for one SNP on 4p16.2, within EVC genes (rs6446395, p = 7.33 × 10-10 ). Rs6446395 also showed significant association with Chinese character reading accuracy (p = 2.95 × 10-4 ), phonological awareness (p = 7.11 × 10-3 ) and rapid automatized naming (p = 4.71 × 10-3 ), implying multiple effects of this variant. The eQTL data showed that rs6446395 affected EVC expression in the cerebellum. Gene-based analyses identified a gene (PRDM10) to be associated with word reading fluency at the genome-wide level. Our study discovered a new candidate susceptibility variant for reading ability and provided new insights into the genetics of developmental dyslexia in Chinese children.
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Affiliation(s)
- Zhengjun Wang
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Shunan Zhao
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Liming Zhang
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Qing Yang
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Chen Cheng
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Ning Ding
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Zijian Zhu
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Hua Shu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Chunyu Liu
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China.,The School of Life Sciences, Central South University, Changsha, China.,Department of Psychiatry, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Jingjing Zhao
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
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4
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Thomas T, Litwin G, Francis DJ, Grigorenko EL. Exploring Genetic and Neural Risk of Specific Reading Disability within a Nuclear Twin Family Case Study: A Translational Clinical Application. J Pers Med 2023; 13. [PMID: 36675818 DOI: 10.3390/jpm13010156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Imaging and genetic studies have characterized biological risk factors contributing to specific reading disability (SRD). The current study aimed to apply this literature to a family of twins discordant for SRD and an older sibling with reading difficulty. Intraclass correlations were used to understand the similarity of imaging phenotypes between pairs. Reading-related genes and brain region phenotypes, including asymmetry indices representing the relative size of left compared to right hemispheric structures, were descriptively examined. SNPs that corresponded between the SRD siblings and not the typically developing (TD) siblings were in genes ZNF385D, LPHN3, CNTNAP2, FGF18, NOP9, CMIP, MYO18B, and RBFOX2. Imaging phenotypes were similar among all sibling pairs for grey matter volume and surface area, but cortical thickness in reading-related regions of interest (ROIs) was more similar among the siblings with SRD, followed by the twins, and then the TD twin and older siblings, suggesting cortical thickness may differentiate risk for this family. The siblings with SRD had more symmetry of cortical thickness in the transverse temporal and superior temporal gyri, while the TD sibling had greater rightward asymmetry. The TD sibling had a greater leftward asymmetry of grey matter volume and cortical surface area in the fusiform, supramarginal, and transverse temporal gyrus. This exploratory study demonstrated that reading-related risk factors appeared to correspond with SRD within this family, suggesting that early examination of biological factors may benefit early identification. Future studies may benefit from the use of polygenic risk scores or machine learning to better understand SRD risk.
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Mountford HS, Braden R, Newbury DF, Morgan AT. The Genetic and Molecular Basis of Developmental Language Disorder: A Review. Children (Basel) 2022; 9:children9050586. [PMID: 35626763 PMCID: PMC9139417 DOI: 10.3390/children9050586] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/28/2022] [Accepted: 04/12/2022] [Indexed: 01/05/2023]
Abstract
Language disorders are highly heritable and are influenced by complex interactions between genetic and environmental factors. Despite more than twenty years of research, we still lack critical understanding of the biological underpinnings of language. This review provides an overview of the genetic landscape of developmental language disorders (DLD), with an emphasis on the importance of defining the specific features (the phenotype) of DLD to inform gene discovery. We review the specific phenotype of DLD in the genetic literature, and the influence of historic variation in diagnostic inclusion criteria on researchers' ability to compare and replicate genotype-phenotype studies. This review provides an overview of the recently identified gene pathways in populations with DLD and explores current state-of-the-art approaches to genetic analysis based on the hypothesised architecture of DLD. We will show how recent global efforts to unify diagnostic criteria have vastly increased sample size and allow for large multi-cohort metanalyses, leading the identification of a growing number of contributory loci. We emphasise the important role of estimating the genetic architecture of DLD to decipher underlying genetic associations. Finally, we explore the potential for epigenetics and environmental interactions to further unravel the biological basis of language disorders.
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Affiliation(s)
- Hayley S. Mountford
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (H.S.M.); (D.F.N.)
| | - Ruth Braden
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne 3052, Australia;
| | - Dianne F. Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (H.S.M.); (D.F.N.)
| | - Angela T. Morgan
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne 3052, Australia;
- Correspondence:
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6
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Bharadwaj H, Mamashli F, Khan S, Singh R, Joseph RM, Losh A, Pawlyszyn S, McGuiggan NM, Graham S, Hämäläinen MS, Kenet T. Cortical signatures of auditory object binding in children with autism spectrum disorder are anomalous in concordance with behavior and diagnosis. PLoS Biol 2022; 20:e3001541. [PMID: 35167585 PMCID: PMC8884487 DOI: 10.1371/journal.pbio.3001541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 02/28/2022] [Accepted: 01/14/2022] [Indexed: 11/24/2022] Open
Abstract
Organizing sensory information into coherent perceptual objects is fundamental to everyday perception and communication. In the visual domain, indirect evidence from cortical responses suggests that children with autism spectrum disorder (ASD) have anomalous figure-ground segregation. While auditory processing abnormalities are common in ASD, especially in environments with multiple sound sources, to date, the question of scene segregation in ASD has not been directly investigated in audition. Using magnetoencephalography, we measured cortical responses to unattended (passively experienced) auditory stimuli while parametrically manipulating the degree of temporal coherence that facilitates auditory figure-ground segregation. Results from 21 children with ASD (aged 7-17 years) and 26 age- and IQ-matched typically developing children provide evidence that children with ASD show anomalous growth of cortical neural responses with increasing temporal coherence of the auditory figure. The documented neurophysiological abnormalities did not depend on age, and were reflected both in the response evoked by changes in temporal coherence of the auditory scene and in the associated induced gamma rhythms. Furthermore, the individual neural measures were predictive of diagnosis (83% accuracy) and also correlated with behavioral measures of ASD severity and auditory processing abnormalities. These findings offer new insight into the neural mechanisms underlying auditory perceptual deficits and sensory overload in ASD, and suggest that temporal-coherence-based auditory scene analysis and suprathreshold processing of coherent auditory objects may be atypical in ASD.
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Affiliation(s)
- Hari Bharadwaj
- Department of Speech, Language, & Hearing Sciences, Purdue University, West Lafayette, Indiana, United States of America
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Fahimeh Mamashli
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
| | - Sheraz Khan
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
| | - Ravinderjit Singh
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Robert M. Joseph
- Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Ainsley Losh
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Stephanie Pawlyszyn
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Nicole M. McGuiggan
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Steven Graham
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Matti S. Hämäläinen
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
| | - Tal Kenet
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
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7
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Nudel R, Appadurai V, Buil A, Nordentoft M, Werge T. Pleiotropy between language impairment and broader behavioral disorders-an investigation of both common and rare genetic variants. J Neurodev Disord 2021; 13:54. [PMID: 34773992 PMCID: PMC8590378 DOI: 10.1186/s11689-021-09403-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Language plays a major role in human behavior. For this reason, neurodevelopmental and psychiatric disorders in which linguistic ability is impaired could have a big impact on the individual's social interaction and general wellbeing. Such disorders tend to have a strong genetic component, but most past studies examined mostly the linguistic overlaps across these disorders; investigations into their genetic overlaps are limited. The aim of this study was to assess the potential genetic overlap between language impairment and broader behavioral disorders employing methods capturing both common and rare genetic variants. METHODS We employ polygenic risk scores (PRS) trained on specific language impairment (SLI) to evaluate genetic overlap across several disorders in a large case-cohort sample comprising ~13,000 autism spectrum disorder (ASD) cases, including cases of childhood autism and Asperger's syndrome, ~15,000 attention deficit/hyperactivity disorder (ADHD) cases, ~3000 schizophrenia cases, and ~21,000 population controls. We also examine rare variants in SLI/language-related genes in a subset of the sample that was exome-sequenced using the SKAT-O method. RESULTS We find that there is little evidence for genetic overlap between SLI and ADHD, schizophrenia, and ASD, the latter being in line with results of linguistic analyses in past studies. However, we observe a small, significant genetic overlap between SLI and childhood autism specifically, which we do not observe for SLI and Asperger's syndrome. Moreover, we observe that childhood autism cases have significantly higher SLI-trained PRS compared to Asperger's syndrome cases; these results correspond well to the linguistic profiles of both disorders. Our rare variant analyses provide suggestive evidence of association for specific genes with ASD, childhood autism, and schizophrenia. CONCLUSIONS Our study provides, for the first time, to our knowledge, genetic evidence for ASD subtypes based on risk variants for language impairment.
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Affiliation(s)
- Ron Nudel
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- CORE - Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Vivek Appadurai
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Alfonso Buil
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- CORE - Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Cao X, Zhang Y, Abdulkadir M, Deng L, Fernandez TV, Garcia-Delgar B, Hagstrøm J, Hoekstra PJ, King RA, Koesterich J, Kuperman S, Morer A, Nasello C, Plessen KJ, Thackray JK, Zhou L, Dietrich A, Tischfield JA, Heiman GA, Xing J. Whole-exome sequencing identifies genes associated with Tourette's disorder in multiplex families. Mol Psychiatry 2021; 26:6937-6951. [PMID: 33837273 PMCID: PMC8501157 DOI: 10.1038/s41380-021-01094-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/17/2021] [Accepted: 03/30/2021] [Indexed: 02/02/2023]
Abstract
Tourette's Disorder (TD) is a neurodevelopmental disorder (NDD) that affects about 0.7% of the population and is one of the most heritable NDDs. Nevertheless, because of its polygenic nature and genetic heterogeneity, the genetic etiology of TD is not well understood. In this study, we combined the segregation information in 13 TD multiplex families with high-throughput sequencing and genotyping to identify genes associated with TD. Using whole-exome sequencing and genotyping array data, we identified both small and large genetic variants within the individuals. We then combined multiple types of evidence to prioritize candidate genes for TD, including variant segregation pattern, variant function prediction, candidate gene expression, protein-protein interaction network, candidate genes from previous studies, etc. From the 13 families, 71 strong candidate genes were identified, including both known genes for NDDs and novel genes, such as HtrA Serine Peptidase 3 (HTRA3), Cadherin-Related Family Member 1 (CDHR1), and Zinc Finger DHHC-Type Palmitoyltransferase 17 (ZDHHC17). The candidate genes are enriched in several Gene Ontology categories, such as dynein complex and synaptic membrane. Candidate genes and pathways identified in this study provide biological insight into TD etiology and potential targets for future studies.
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Affiliation(s)
- Xiaolong Cao
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA,Human Genetic Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Yeting Zhang
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA,Human Genetic Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Mohamed Abdulkadir
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA,Human Genetic Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA,Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Li Deng
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA,Human Genetic Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Thomas V. Fernandez
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, USA,Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Blanca Garcia-Delgar
- Department of Child and Adolescent Psychiatry, and Psychology, Institute of Neurosciences, Hospital Clinic, Universitari, Barcelona, Spain
| | - Julie Hagstrøm
- Child and Adolescent Mental Health Center, Mental Health Services, Capital Region of Denmark, Denmark
| | - Pieter J. Hoekstra
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Robert A. King
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, USA
| | - Justin Koesterich
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA,Human Genetic Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Samuel Kuperman
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Astrid Morer
- Department of Child and Adolescent Psychiatry, and Psychology, Institute of Neurosciences, Hospital Clinic, Universitari, Barcelona, Spain,Institut d’Investigacions Biomediques August Pi i Sunyer, (IDIPABS), Barcelona, Spain,Centro de Investigacion en Red de Salud Mental (CIBERSAM), Instituto Carlos III, Spain
| | - Cara Nasello
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA,Human Genetic Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Kerstin J. Plessen
- Child and Adolescent Mental Health Center, Mental Health Services, Capital Region of Denmark, Denmark,Division of Child and Adolescent Psychiatry, University Hospital Lausanne, Switzerland
| | - Joshua K. Thackray
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA,Human Genetic Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Lisheng Zhou
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | | | - Andrea Dietrich
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jay A. Tischfield
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA,Human Genetic Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Gary A. Heiman
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA,Human Genetic Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA. .,Human Genetic Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
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9
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Thomas T, Khalaf S, Grigorenko EL. A systematic review and meta-analysis of imaging genetics studies of specific reading disorder. Cogn Neuropsychol 2021; 38:179-204. [PMID: 34529546 DOI: 10.1080/02643294.2021.1969900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The imaging genetics of specific reading disabilities (SRD) is an emerging field that aims to characterize the disabilities' neurobiological causes, including atypical brain structure and function and distinct genetic architecture. The present review aimed to summarize current imaging genetics studies of SRD, characterize the effect sizes of reported results by calculating Cohen's d, complete a Fisher's Combined Probability Test for genes featured in multiple studies, and determine areas for future research. Results demonstrate associations between SRD risk genes and reading network brain phenotypes. The Fisher's test revealed promising results for the genes DCDC2, KIAA0319, FOXP2, SLC2A3, and ROBO1. Future research should focus on exploratory approaches to identify previously undiscovered genes. Using comprehensive neuroimaging (e.g., functional and effective connectivity) and genetic (e.g., sequencing and epigenetic) techniques, and using larger samples, diverse stages of development, and longitudinal investigations, would help researchers understand the neurobiological correlates of SRD to improve early identification.
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Affiliation(s)
- Tina Thomas
- Department of Psychology, University of Houston, Houston, TX, USA.,Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, TX, USA
| | - Shiva Khalaf
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, TX, USA
| | - Elena L Grigorenko
- Department of Psychology, University of Houston, Houston, TX, USA.,Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, TX, USA.,Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Unger N, Heim S, Hilger DI, Bludau S, Pieperhoff P, Cichon S, Amunts K, Mühleisen TW. Identification of Phonology-Related Genes and Functional Characterization of Broca's and Wernicke's Regions in Language and Learning Disorders. Front Neurosci 2021; 15:680762. [PMID: 34539327 PMCID: PMC8446646 DOI: 10.3389/fnins.2021.680762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/04/2021] [Indexed: 12/02/2022] Open
Abstract
Impaired phonological processing is a leading symptom of multifactorial language and learning disorders suggesting a common biological basis. Here we evaluated studies of dyslexia, dyscalculia, specific language impairment (SLI), and the logopenic variant of primary progressive aphasia (lvPPA) seeking for shared risk genes in Broca's and Wernicke's regions, being key for phonological processing within the complex language network. The identified "phonology-related genes" from literature were functionally characterized using Atlas-based expression mapping (JuGEx) and gene set enrichment. Out of 643 publications from the last decade until now, we extracted 21 candidate genes of which 13 overlapped with dyslexia and SLI, six with dyslexia and dyscalculia, and two with dyslexia, dyscalculia, and SLI. No overlap was observed between the childhood disorders and the late-onset lvPPA often showing symptoms of learning disorders earlier in life. Multiple genes were enriched in Gene Ontology terms of the topics learning (CNTNAP2, CYFIP1, DCDC2, DNAAF4, FOXP2) and neuronal development (CCDC136, CNTNAP2, CYFIP1, DCDC2, KIAA0319, RBFOX2, ROBO1). Twelve genes showed above-average expression across both regions indicating moderate-to-high gene activity in the investigated cortical part of the language network. Of these, three genes were differentially expressed suggesting potential regional specializations: ATP2C2 was upregulated in Broca's region, while DNAAF4 and FOXP2 were upregulated in Wernicke's region. ATP2C2 encodes a magnesium-dependent calcium transporter which fits with reports about disturbed calcium and magnesium levels for dyslexia and other communication disorders. DNAAF4 (formerly known as DYX1C1) is involved in neuronal migration supporting the hypothesis of disturbed migration in dyslexia. FOXP2 is a transcription factor that regulates a number of genes involved in development of speech and language. Overall, our interdisciplinary and multi-tiered approach provided evidence that genetic and transcriptional variation of ATP2C2, DNAAF4, and FOXP2 may play a role in physiological and pathological aspects of phonological processing.
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Affiliation(s)
- Nina Unger
- Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Department of Neurology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Stefan Heim
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty, RWTH Aachen University, Aachen, Germany
- JARA-Brain, Jülich-Aachen Research Alliance, Jülich, Germany
| | - Dominique I. Hilger
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
| | - Sebastian Bludau
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
| | - Peter Pieperhoff
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
| | - Sven Cichon
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Katrin Amunts
- Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- JARA-Brain, Jülich-Aachen Research Alliance, Jülich, Germany
| | - Thomas W. Mühleisen
- Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Department of Biomedicine, University of Basel, Basel, Switzerland
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11
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Lancaster HS, Li J, Gray S. Selective visual attention skills differentially predict decoding and reading comprehension performance across reading ability profiles. J Res Read 2021; 44:715-734. [PMID: 35557998 PMCID: PMC9090198 DOI: 10.1111/1467-9817.12368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND The purpose of this study was to examine the relationship between selective visual attention (SVA), reading decoding, listening comprehension and reading comprehension in children with and without a reading disorder. METHODS We used longitudinal data from the Avon Longitudinal Study of Parents and Children. We split children into four groups: Typical Readers, Dyslexics, Poor Comprehenders and Comorbid Reading Disorder. We included measures of single word reading, nonword reading, spelling, phonological processing, vocabulary, receptive language, nonverbal intelligence, selective attention and reading comprehension. We used analysis of variance, correlations and structural equation modelling to examine the relationship between SVA and reading. We fit two possible models: SVA Indirect and SVA Direct. The difference between these models was the inclusion of a direct path from SVA to reading comprehension. RESULTS We examined an indirect model, where SVA predicted reading comprehension through word decoding and listening comprehension, and a direct model, which included a pathway from SVA to reading comprehension. Based on our analysis of variance and correlation results, we collapsed the Dyslexic, Poor Comprehenders and Comorbid Reading Disorder groups for the structural equation modelling. We found evidence that for Typical Readers, an indirect model was the best fit, whereas the direct model was the best model for children with a reading disorder. CONCLUSIONS Selective visual attention is related to reading comprehension. This relationship differs for children with and without a reading disorder.
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Affiliation(s)
- Hope Sparks Lancaster
- Center of Childhood Deafness, Language, and Learning, Boys Town National Research Hospital, Omaha, NE, USA and Program of Speech and Hearing Science, College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Jing Li
- H. Milton Stewart School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shelley Gray
- Program of Speech and Hearing Science, College of Health Solutions, Arizona State University, Phoenix, AZ, USA
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12
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Benchek P, Igo RP, Voss-Hoynes H, Wren Y, Miller G, Truitt B, Zhang W, Osterman M, Freebairn L, Tag J, Taylor HG, Chan ER, Roussos P, Lewis B, Stein CM, Iyengar SK. Association between genes regulating neural pathways for quantitative traits of speech and language disorders. NPJ Genom Med 2021; 6:64. [PMID: 34315907 PMCID: PMC8316336 DOI: 10.1038/s41525-021-00225-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
Speech sound disorders (SSD) manifest as difficulties in phonological memory and awareness, oral motor function, language, vocabulary, reading, and spelling. Families enriched for SSD are rare, and typically display a cluster of deficits. We conducted a genome-wide association study (GWAS) in 435 children from 148 families in the Cleveland Family Speech and Reading study (CFSRS), examining 16 variables representing 6 domains. Replication was conducted using the Avon Longitudinal Study of Parents and Children (ALSPAC). We identified 18 significant loci (combined p < 10-8) that we pursued bioinformatically. We prioritized 5 novel gene regions with likely functional repercussions on neural pathways, including those which colocalized with differentially methylated regions in our sample. Polygenic risk scores for receptive language, expressive vocabulary, phonological awareness, phonological memory, spelling, and reading decoding associated with increasing clinical severity. In summary, neural-genetic influence on SSD is primarily multigenic and acts on genomic regulatory elements, similar to other neurodevelopmental disorders.
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Affiliation(s)
- Penelope Benchek
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Robert P Igo
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Heather Voss-Hoynes
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Yvonne Wren
- Bristol Dental School, Faculty of Health Sciences, University of Bristol, and Bristol Speech and Language Therapy Research Unit, North Bristol NHS Trust, Bristol, UK
| | - Gabrielle Miller
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Barbara Truitt
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Wen Zhang
- Department of Psychiatry, Friedman Brain Institute, and Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Osterman
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Lisa Freebairn
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Jessica Tag
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - H Gerry Taylor
- Department of Pediatrics, Case Western Reserve University, and Rainbow Babies & Children's Hospital, University Hospital Case Medical Center, Cleveland, OH, USA
- Nationwide Children's Hospital Research Institute and Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - E Ricky Chan
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Panos Roussos
- Department of Psychiatry, Friedman Brain Institute, and Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Barbara Lewis
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Hearing and Speech Center, Cleveland, OH, USA
| | - Catherine M Stein
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
| | - Sudha K Iyengar
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
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Martinelli A, Rice ML, Talcott JB, Diaz R, Smith S, Raza MH, Snowling MJ, Hulme C, Stein J, Hayiou-Thomas ME, Hawi Z, Kent L, Pitt SJ, Newbury DF, Paracchini S. A rare missense variant in the ATP2C2 gene is associated with language impairment and related measures. Hum Mol Genet 2021; 30:1160-1171. [PMID: 33864365 PMCID: PMC8188402 DOI: 10.1093/hmg/ddab111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/02/2023] Open
Abstract
At least 5% of children present unexpected difficulties in expressing and understanding spoken language. This condition is highly heritable and often co-occurs with other neurodevelopmental disorders such as dyslexia and ADHD. Through an exome sequencing analysis, we identified a rare missense variant (chr16:84405221, GRCh38.p12) in the ATP2C2 gene. ATP2C2 was implicated in language disorders by linkage and association studies, and exactly the same variant was reported previously in a different exome sequencing study for language impairment (LI). We followed up this finding by genotyping the mutation in cohorts selected for LI and comorbid disorders. We found that the variant had a higher frequency in LI cases (1.8%, N = 360) compared with cohorts selected for dyslexia (0.8%, N = 520) and ADHD (0.7%, N = 150), which presented frequencies comparable to reference databases (0.9%, N = 24 046 gnomAD controls). Additionally, we observed that carriers of the rare variant identified from a general population cohort (N = 42, ALSPAC cohort) presented, as a group, lower scores on a range of reading and language-related measures compared to controls (N = 1825; minimum P = 0.002 for non-word reading). ATP2C2 encodes for an ATPase (SPCA2) that transports calcium and manganese ions into the Golgi lumen. Our functional characterization suggested that the rare variant influences the ATPase activity of SPCA2. Thus, our results further support the role of ATP2C2 locus in language-related phenotypes and pinpoint the possible effects of a specific rare variant at molecular level.
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Affiliation(s)
| | - Mabel L Rice
- Child Language Doctoral Program, University of Kansas, Lawrence, KS, USA
| | - Joel B Talcott
- Aston Brain Centre, School of Life and Health Sciences, Aston University, Birmingham, UK
| | - Rebeca Diaz
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Shelley Smith
- Department of Neurological Sciences, University of Nebraska Medical Center, Lincoln, NE, USA
| | | | - Margaret J Snowling
- Department of Experimental Psychology and St John's College, University of Oxford, Oxford, UK
| | - Charles Hulme
- Department of Education, University of Oxford, Oxford, UK
| | - John Stein
- Department of Physiology, University of Oxford, Oxford, UK
| | | | - Ziarih Hawi
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, VIC, Australia
| | - Lindsey Kent
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Samantha J Pitt
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Dianne F Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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Carrion-Castillo A, Estruch SB, Maassen B, Franke B, Francks C, Fisher SE. Whole-genome sequencing identifies functional noncoding variation in SEMA3C that cosegregates with dyslexia in a multigenerational family. Hum Genet 2021; 140:1183-200. [PMID: 34076780 DOI: 10.1007/s00439-021-02289-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/27/2021] [Indexed: 12/11/2022]
Abstract
Dyslexia is a common heritable developmental disorder involving impaired reading abilities. Its genetic underpinnings are thought to be complex and heterogeneous, involving common and rare genetic variation. Multigenerational families segregating apparent monogenic forms of language-related disorders can provide useful entrypoints into biological pathways. In the present study, we performed a genome-wide linkage scan in a three-generational family in which dyslexia affects 14 of its 30 members and seems to be transmitted with an autosomal dominant pattern of inheritance. We identified a locus on chromosome 7q21.11 which cosegregated with dyslexia status, with the exception of two cases of phenocopy (LOD = 2.83). Whole-genome sequencing of key individuals enabled the assessment of coding and noncoding variation in the family. Two rare single-nucleotide variants (rs144517871 and rs143835534) within the first intron of the SEMA3C gene cosegregated with the 7q21.11 risk haplotype. In silico characterization of these two variants predicted effects on gene regulation, which we functionally validated for rs144517871 in human cell lines using luciferase reporter assays. SEMA3C encodes a secreted protein that acts as a guidance cue in several processes, including cortical neuronal migration and cellular polarization. We hypothesize that these intronic variants could have a cis-regulatory effect on SEMA3C expression, making a contribution to dyslexia susceptibility in this family.
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15
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Georgitsi M, Dermitzakis I, Soumelidou E, Bonti E. The Polygenic Nature and Complex Genetic Architecture of Specific Learning Disorder. Brain Sci 2021; 11:631. [PMID: 34068951 DOI: 10.3390/brainsci11050631] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/16/2022] Open
Abstract
Specific Learning Disorder (SLD) is a multifactorial, neurodevelopmental disorder which may involve persistent difficulties in reading (dyslexia), written expression and/or mathematics. Dyslexia is characterized by difficulties with speed and accuracy of word reading, deficient decoding abilities, and poor spelling. Several studies from different, but complementary, scientific disciplines have investigated possible causal/risk factors for SLD. Biological, neurological, hereditary, cognitive, linguistic-phonological, developmental and environmental factors have been incriminated. Despite worldwide agreement that SLD is highly heritable, its exact biological basis remains elusive. We herein present: (a) an update of studies that have shaped our current knowledge on the disorder’s genetic architecture; (b) a discussion on whether this genetic architecture is ‘unique’ to SLD or, alternatively, whether there is an underlying common genetic background with other neurodevelopmental disorders; and, (c) a brief discussion on whether we are at a position of generating meaningful correlations between genetic findings and anatomical data from neuroimaging studies or specific molecular/cellular pathways. We conclude with open research questions that could drive future research directions.
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Thomas T, Perdue MV, Khalaf S, Landi N, Hoeft F, Pugh K, Grigorenko EL. Neuroimaging genetic associations between SEMA6D, brain structure, and reading skills. J Clin Exp Neuropsychol 2021; 43:276-289. [PMID: 33960276 PMCID: PMC8225580 DOI: 10.1080/13803395.2021.1912300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/30/2021] [Indexed: 01/15/2023]
Abstract
Specific reading disability (SRD) is defined by genetic and neural risk factors that are not fully understood. The current study used imaging genetics methodology to investigate relationships between SEMA6D, brain structure, and reading. SEMA6D, located on SRD risk locus DYX1, is involved in axon guidance, synapse formation, and dendrite development. SEMA6D's associations with brain structure in reading-related regions of interest (ROIs) were investigated in a sample of children with a range of reading performance, from sites in Connecticut, CT (n = 67, 6-13 years, mean age = 9.07) and San Francisco, SF (n = 28, 5-8 years, mean age = 6.5). Multiple regression analyses revealed significant associations between SEMA6D's rs16959669 and cortical thickness in the fusiform gyrus and rs4270119 and gyrification in the supramarginal gyrus in the CT sample, but this was not replicated in the SF sample. Significant clusters were not associated with reading. For white matter volume, combined analyses across both samples revealed associations between reading and the left transverse temporal gyrus, left pars triangularis, left cerebellum, and right cerebellum. White matter volume in the left transverse temporal gyrus was nominally related to rs1817178, rs12050859, and rs1898110 in SEMA6D, and rs1817178 was significantly related to reading. Haplotype analyses revealed significant associations between the whole gene and brain phenotypes. Results suggest SEMA6D likely has an impact on multiple reading-related neural structures, but only white matter volume in the transverse temporal gyrus was significantly related to reading in the current sample. As the sample was young, the transverse temporal gyrus, involved in auditory perception, may be more strongly involved in reading because phonological processing is still being learned. The relationship between SEMA6D and reading may change as different brain regions are involved during reading development. Future research should examine mediating effects, use additional brain measures, and use an older sample to better understand effects.
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Affiliation(s)
- Tina Thomas
- Department of Psychology, University of Houston, Houston, TX, USA
| | - Meaghan V. Perdue
- University of Connecticut Dept. of Psychological Sciences, Storrs, CT, USA
- Haskins Laboratories, University of Connecticut, New Haven, CT, USA
| | - Shiva Khalaf
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, TX, USA
| | - Nicole Landi
- University of Connecticut Dept. of Psychological Sciences, Storrs, CT, USA
- Haskins Laboratories, University of Connecticut, New Haven, CT, USA
| | - Fumiko Hoeft
- University of Connecticut Dept. of Psychological Sciences, Storrs, CT, USA
- Department of Psychiatry, University of California, San Francisco, CA, USA
| | - Kenneth Pugh
- University of Connecticut Dept. of Psychological Sciences, Storrs, CT, USA
- Haskins Laboratories, University of Connecticut, New Haven, CT, USA
| | - Elena L. Grigorenko
- Department of Psychology, University of Houston, Houston, TX, USA
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, TX, USA
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Gialluisi A, Andlauer TFM, Mirza-Schreiber N, Moll K, Becker J, Hoffmann P, Ludwig KU, Czamara D, Pourcain BS, Honbolygó F, Tóth D, Csépe V, Huguet G, Chaix Y, Iannuzzi S, Demonet JF, Morris AP, Hulslander J, Willcutt EG, DeFries JC, Olson RK, Smith SD, Pennington BF, Vaessen A, Maurer U, Lyytinen H, Peyrard-Janvid M, Leppänen PHT, Brandeis D, Bonte M, Stein JF, Talcott JB, Fauchereau F, Wilcke A, Kirsten H, Müller B, Francks C, Bourgeron T, Monaco AP, Ramus F, Landerl K, Kere J, Scerri TS, Paracchini S, Fisher SE, Schumacher J, Nöthen MM, Müller-Myhsok B, Schulte-Körne G. Genome-wide association study reveals new insights into the heritability and genetic correlates of developmental dyslexia. Mol Psychiatry 2021; 26:3004-17. [PMID: 33057169 DOI: 10.1038/s41380-020-00898-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 07/26/2020] [Accepted: 09/18/2020] [Indexed: 02/06/2023]
Abstract
Developmental dyslexia (DD) is a learning disorder affecting the ability to read, with a heritability of 40-60%. A notable part of this heritability remains unexplained, and large genetic studies are warranted to identify new susceptibility genes and clarify the genetic bases of dyslexia. We carried out a genome-wide association study (GWAS) on 2274 dyslexia cases and 6272 controls, testing associations at the single variant, gene, and pathway level, and estimating heritability using single-nucleotide polymorphism (SNP) data. We also calculated polygenic scores (PGSs) based on large-scale GWAS data for different neuropsychiatric disorders and cortical brain measures, educational attainment, and fluid intelligence, testing them for association with dyslexia status in our sample. We observed statistically significant (p < 2.8 × 10-6) enrichment of associations at the gene level, for LOC388780 (20p13; uncharacterized gene), and for VEPH1 (3q25), a gene implicated in brain development. We estimated an SNP-based heritability of 20-25% for DD, and observed significant associations of dyslexia risk with PGSs for attention deficit hyperactivity disorder (at pT = 0.05 in the training GWAS: OR = 1.23[1.16; 1.30] per standard deviation increase; p = 8 × 10-13), bipolar disorder (1.53[1.44; 1.63]; p = 1 × 10-43), schizophrenia (1.36[1.28; 1.45]; p = 4 × 10-22), psychiatric cross-disorder susceptibility (1.23[1.16; 1.30]; p = 3 × 10-12), cortical thickness of the transverse temporal gyrus (0.90[0.86; 0.96]; p = 5 × 10-4), educational attainment (0.86[0.82; 0.91]; p = 2 × 10-7), and intelligence (0.72[0.68; 0.76]; p = 9 × 10-29). This study suggests an important contribution of common genetic variants to dyslexia risk, and novel genomic overlaps with psychiatric conditions like bipolar disorder, schizophrenia, and cross-disorder susceptibility. Moreover, it revealed the presence of shared genetic foundations with a neural correlate previously implicated in dyslexia by neuroimaging evidence.
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Koshiba S, Motoike IN, Saigusa D, Inoue J, Aoki Y, Tadaka S, Shirota M, Katsuoka F, Tamiya G, Minegishi N, Fuse N, Kinoshita K, Yamamoto M. Identification of critical genetic variants associated with metabolic phenotypes of the Japanese population. Commun Biol 2020; 3:662. [PMID: 33177615 PMCID: PMC7659008 DOI: 10.1038/s42003-020-01383-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 10/18/2020] [Indexed: 02/07/2023] Open
Abstract
We performed a metabolome genome-wide association study for the Japanese population in the prospective cohort study of Tohoku Medical Megabank. By combining whole-genome sequencing and nontarget metabolome analyses, we identified a large number of novel associations between genetic variants and plasma metabolites. Of the identified metabolite-associated genes, approximately half have already been shown to be involved in various diseases. We identified metabolite-associated genes involved in the metabolism of xenobiotics, some of which are from intestinal microorganisms, indicating that the identified genetic variants also markedly influence the interaction between the host and symbiotic bacteria. We also identified five associations that appeared to be female-specific. A number of rare variants that influence metabolite levels were also found, and combinations of common and rare variants influenced the metabolite levels more profoundly. These results support our contention that metabolic phenotyping provides important insights into how genetic and environmental factors provoke human diseases.
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Affiliation(s)
- Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
| | - Jin Inoue
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579, Japan
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579, Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
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19
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Lancaster HS, Liu X, Dinu V, Li J. Identifying interactive biological pathways associated with reading disability. Brain Behav 2020; 10:e01735. [PMID: 32596987 PMCID: PMC7428467 DOI: 10.1002/brb3.1735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Past research has suggested that reading disability is a complex disorder involving genetic and environment contributions, as well as gene-gene and gene-environment interaction, but to date little is known about the underlying mechanisms. METHOD Using the Avon Longitudinal Study of Parents and Children, we assessed the contributions of genetic, demographic, and environmental variables on case-control status using machine learning. We investigated the functional interactions between genes using pathway and network analysis. RESULTS Our results support a systems approach to studying the etiology of reading disability with many genes (e.g., RAPGEF2, KIAA0319, DLC1) and biological pathways (e.g., neuron migration, positive regulation of dendrite regulation, nervous system development) interacting with each other. We found that single nucleotide variants within genes often had opposite effects and that enriched biological pathways were mediated by neuron migration. We also identified behavioral (i.e., receptive language, nonverbal intelligence, and vocabulary), demographic (i.e., mother's highest education), and environmental (i.e., birthweight) factors that influenced case-control status when accounting for genetic information. DISCUSSION The behavioral and demographic factors were suggested to be protective against reading disability status, while birthweight conveyed risk. We provided supporting evidence that reading disability has a complex biological and environmental etiology and that there may be a shared genetic and neurobiological architecture for reading (dis)ability.
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Affiliation(s)
- Hope Sparks Lancaster
- College of Health SolutionsArizona State UniversityTempeAZUSA
- Department of Computing, Informatics, and Decision Systems EngineeringSchools of EngineeringArizona State UniversityTempeAZUSA
| | - Xiaonan Liu
- Department of Computing, Informatics, and Decision Systems EngineeringSchools of EngineeringArizona State UniversityTempeAZUSA
| | - Valentin Dinu
- College of Health SolutionsArizona State UniversityTempeAZUSA
| | - Jing Li
- School of Industrial and Systems EngineeringGeorgia Institute of TechnologyAtlantaGAUSA
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20
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Nudel R, Christiani CAJ, Ohland J, Uddin MJ, Hemager N, Ellersgaard D, Spang KS, Burton BK, Greve AN, Gantriis DL, Bybjerg-Grauholm J, Jepsen JRM, Thorup AAE, Mors O, Werge T, Nordentoft M. Quantitative genome-wide association analyses of receptive language in the Danish High Risk and Resilience Study. BMC Neurosci 2020; 21:30. [PMID: 32635940 PMCID: PMC7341668 DOI: 10.1186/s12868-020-00581-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/28/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND One of the most basic human traits is language. Linguistic ability, and disability, have been shown to have a strong genetic component in family and twin studies, but molecular genetic studies of language phenotypes are scarce, relative to studies of other cognitive traits and neurodevelopmental phenotypes. Moreover, most genetic studies examining such phenotypes do not incorporate parent-of-origin effects, which could account for some of the heritability of the investigated trait. We performed a genome-wide association study of receptive language, examining both child genetic effects and parent-of-origin effects. RESULTS Using a family-based cohort with 400 children with receptive language scores, we found a genome-wide significant paternal parent-of-origin effect with a SNP, rs11787922, on chromosome 9q21.31, whereby the T allele reduced the mean receptive language score by ~ 23, constituting a reduction of more than 1.5 times the population SD (P = 1.04 × 10-8). We further confirmed that this association was not driven by broader neurodevelopmental diagnoses in the child or a family history of psychiatric diagnoses by incorporating covariates for the above and repeating the analysis. CONCLUSIONS Our study reports a genome-wide significant association for receptive language skills; to our knowledge, this is the first documented genome-wide significant association for this phenotype. Furthermore, our study illustrates the importance of considering parent-of-origin effects in association studies, particularly in the case of cognitive or neurodevelopmental traits, in which parental genetic data are not always incorporated.
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Affiliation(s)
- Ron Nudel
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
| | - Camilla A J Christiani
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Jessica Ohland
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Md Jamal Uddin
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
- Section for Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Nicoline Hemager
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Ditte Ellersgaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Katrine S Spang
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Birgitte K Burton
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Aja N Greve
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Ditte L Gantriis
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jens Richardt M Jepsen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
- Center for Neuropsychiatric Schizophrenia Research and Center for Clinical Intervention and Neuropsychiatric Schizophrenia Research, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Anne A E Thorup
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark.
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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21
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Lu Y, Shiau F, Yi W, Lu S, Wu Q, Pearson JD, Kallman A, Zhong S, Hoang T, Zuo Z, Zhao F, Zhang M, Tsai N, Zhuo Y, He S, Zhang J, Stein-O'Brien GL, Sherman TD, Duan X, Fertig EJ, Goff LA, Zack DJ, Handa JT, Xue T, Bremner R, Blackshaw S, Wang X, Clark BS. Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development. Dev Cell 2020; 53:473-491.e9. [PMID: 32386599 DOI: 10.1016/j.devcel.2020.04.009] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/05/2020] [Accepted: 04/10/2020] [Indexed: 01/08/2023]
Abstract
The development of single-cell RNA sequencing (scRNA-seq) has allowed high-resolution analysis of cell-type diversity and transcriptional networks controlling cell-fate specification. To identify the transcriptional networks governing human retinal development, we performed scRNA-seq analysis on 16 time points from developing retina as well as four early stages of retinal organoid differentiation. We identified evolutionarily conserved patterns of gene expression during retinal progenitor maturation and specification of all seven major retinal cell types. Furthermore, we identified gene-expression differences between developing macula and periphery and between distinct populations of horizontal cells. We also identified species-specific patterns of gene expression during human and mouse retinal development. Finally, we identified an unexpected role for ATOH7 expression in regulation of photoreceptor specification during late retinogenesis. These results provide a roadmap to future studies of human retinal development and may help guide the design of cell-based therapies for treating retinal dystrophies.
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22
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Abstract
PURPOSE OF REVIEW To better understand the shared basis of language and mental health, this review examines the behavioral and neurobiological features of aberrant language in five major neuropsychiatric conditions. Special attention is paid to genes implicated in both language and neuropsychiatric disorders, as they reveal biological domains likely to underpin the processes controlling both. RECENT FINDINGS Abnormal language and communication are common manifestations of neuropsychiatric conditions, and children with impaired language are more likely to develop psychiatric disorders than their peers. Major themes in the genetics of both language and psychiatry include master transcriptional regulators, like FOXP2; key developmental regulators, like AUTS2; and mediators of neurotransmission, like GRIN2A and CACNA1C.
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23
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Rakhlin N, Landi N, Lee M, Magnuson JS, Naumova OY, Ovchinnikova IV, Grigorenko EL. Cohesion of Cortical Language Networks During Word Processing Is Predicted by a Common Polymorphism in the
SETBP1
Gene. New Dir Child Adolesc Dev 2020; 2020:131-155. [DOI: 10.1002/cad.20331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | | | | | | | | | - Elena L. Grigorenko
- Haskins Laboratories
- Yale University
- University of Houston
- Saint-Petersburg State University
- Moscow State University for Psychology and Education
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24
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Gouveia MH, Cesar CC, Santolalla ML, Anna HPS, Scliar MO, Leal TP, Araújo NM, Soares-Souza GB, Magalhães WCS, Mata IF, Ferri CP, Castro-Costa E, Mbulaiteye SM, Tishkoff SA, Shriner D, Rotimi CN, Tarazona-Santos E, Lima-Costa MF. Genetics of cognitive trajectory in Brazilians: 15 years of follow-up from the Bambuí-Epigen Cohort Study of Aging. Sci Rep 2019; 9:18085. [PMID: 31792241 PMCID: PMC6889148 DOI: 10.1038/s41598-019-53988-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/07/2019] [Indexed: 01/11/2023] Open
Abstract
Age-related cognitive decline (ACD) is the gradual process of decreasing of cognitive function over age. Most genetic risk factors for ACD have been identified in European populations and there are no reports in admixed Latin American individuals. We performed admixture mapping, genome-wide association analysis (GWAS), and fine-mapping to examine genetic factors associated with 15-year cognitive trajectory in 1,407 Brazilian older adults, comprising 14,956 Mini-Mental State Examination measures. Participants were enrolled as part of the Bambuí-Epigen Cohort Study of Aging. Our admixture mapping analysis identified a genomic region (3p24.2) in which increased Native American ancestry was significantly associated with faster ACD. Fine-mapping of this region identified a single nucleotide polymorphism (SNP) rs142380904 (β = -0.044, SE = 0.01, p = 7.5 × 10-5) associated with ACD. In addition, our GWAS identified 24 associated SNPs, most in genes previously reported to influence cognitive function. The top six associated SNPs accounted for 18.5% of the ACD variance in our data. Furthermore, our longitudinal study replicated previous GWAS hits for cognitive decline and Alzheimer's disease. Our 15-year longitudinal study identified both ancestry-specific and cosmopolitan genetic variants associated with ACD in Brazilians, highlighting the need for more trans-ancestry genomic studies, especially in underrepresented ethnic groups.
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Affiliation(s)
- Mateus H Gouveia
- Fundação Oswaldo Cruz, Instituto de Pesquisas René Rachou, Belo Horizonte, Brazil.
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil.
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
| | - Cibele C Cesar
- Universidade Federal de Minas Gerais, Faculdade de Ciências Econômicas, Belo Horizonte, Brazil
| | - Meddly L Santolalla
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Hanaisa P Sant Anna
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
- Melbourne Integrative Genomics, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Marilia O Scliar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Thiago P Leal
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Nathalia M Araújo
- Fundação Oswaldo Cruz, Instituto de Pesquisas René Rachou, Belo Horizonte, Brazil
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Giordano B Soares-Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Wagner C S Magalhães
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
- Núcleo de Ensino e Pesquisa - NEP, Instituto Mário Penna, Rua Gentios, Terceiro Andar, Belo Horizonte, Minas Gerais, 3052, Brazil
| | - Ignacio F Mata
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Cleusa P Ferri
- Universidade Federal de São Paulo, Department of Psychiatry, São Paulo, Brazil
| | - Erico Castro-Costa
- Fundação Oswaldo Cruz, Instituto de Pesquisas René Rachou, Belo Horizonte, Brazil
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
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25
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Nudel R, Christiani CAJ, Ohland J, Uddin MJ, Hemager N, Ellersgaard DV, Spang KS, Burton BK, Greve AN, Gantriis DL, Bybjerg-Grauholm J, Jepsen JRM, Thorup AAE, Mors O, Nordentoft M, Werge T. Language deficits in specific language impairment, attention deficit/hyperactivity disorder, and autism spectrum disorder: An analysis of polygenic risk. Autism Res 2019; 13:369-381. [PMID: 31577390 PMCID: PMC7078922 DOI: 10.1002/aur.2211] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/04/2019] [Indexed: 12/27/2022]
Abstract
Language is one of the cognitive domains often impaired across many neurodevelopmental disorders. While for some disorders the linguistic deficit is the primary impairment (e.g., specific language impairment, SLI), for others it may accompany broader behavioral problems (e.g., autism). The precise nature of this phenotypic overlap has been the subject of debate. Moreover, several studies have found genetic overlaps across neurodevelopmental disorders. This raises the question of whether these genetic overlaps may correlate with phenotypic overlaps and, if so, in what manner. Here, we apply a genome‐wide approach to the study of the linguistic deficit in SLI, autism spectrum disorder (ASD), and attention deficit/hyperactivity disorder (ADHD). Using a discovery genome‐wide association study of SLI, we generate polygenic risk scores (PRS) in an independent sample which includes children with language impairment, SLI, ASD or ADHD and age‐matched controls and perform regression analyses across groups. The SLI‐trained PRS significantly predicted risk in the SLI case–control group (adjusted R2 = 6.24%; P = 0.024) but not in the ASD or ADHD case‐control groups (adjusted R2 = 0.0004%, 0.01%; P = 0.984, 0.889, respectively) nor for height, used as a negative control (R2 = 0.2%; P = 0.452). Additionally, there was a significant difference in the normalized PRS between children with SLI and children with ASD (common language effect size = 0.66; P = 0.044). Our study suggests no additive common‐variant genetic overlap between SLI and ASD and ADHD. This is discussed in the context of phenotypic studies of SLI and related disorders. Autism Res 2020, 13: 369–381. © 2019 The Authors. Autism Research published by International Society for Autism Research published by Wiley Periodicals, Inc. Lay Summary Language deficits are characteristic of specific language impairment (SLI), but may also be found in other neurodevelopmental disorders, such as autism spectrum disorder (ASD) and attention deficit/hyperactivity disorder (ADHD). Many studies examined the overlaps and differences across the language deficits in these disorders, but few studies have examined the genetic aspect thereof. In this study, we use a genome‐wide approach to evaluate whether common genetic variants increasing risk of SLI may also be associated with ASD and ADHD in the same manner. Our results suggest that this is not the case, and we discuss this finding in the context of theories concerning the etiologies of these disorders.
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Affiliation(s)
- Ron Nudel
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Camilla A J Christiani
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Jessica Ohland
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Md Jamal Uddin
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark.,Section for Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Nicoline Hemager
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Ditte V Ellersgaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Katrine S Spang
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre for Child and Adolescent Psychiatry - Research Unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Birgitte K Burton
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre for Child and Adolescent Psychiatry - Research Unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Aja N Greve
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Ditte L Gantriis
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jens Richardt M Jepsen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark.,Mental Health Centre for Child and Adolescent Psychiatry - Research Unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark.,Center for Neuropsychiatric Schizophrenia Research and Center for Clinical Intervention and Neuropsychiatric Schizophrenia Research, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Anne A E Thorup
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre for Child and Adolescent Psychiatry - Research Unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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26
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Liu L, Gu H, Hou F, Xie X, Li X, Zhu B, Zhang J, Wei WH, Song R. Dyslexia associated functional variants in Europeans are not associated with dyslexia in Chinese. Am J Med Genet B Neuropsychiatr Genet 2019; 180:488-495. [PMID: 31264768 DOI: 10.1002/ajmg.b.32750] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/30/2019] [Accepted: 06/14/2019] [Indexed: 01/09/2023]
Abstract
Genome-wide association studies (GWAS) of developmental dyslexia (DD) often used European samples and identified only a handful associations with moderate or weak effects. This study aims to identify DD functional variants by integrating the GWAS associations with tissue-specific functional data and test the variants in a Chinese DD study cohort named READ. We colocalized associations from nine DD related GWAS with expression quantitative trait loci (eQTL) derived from brain tissues and identified two eSNPs rs349045 and rs201605. Both eSNPs had supportive evidence of chromatin interactions observed in human hippocampus tissues and their respective target genes ZNF45 and DNAH9 both had lower expression in brain tissues in schizophrenia patients than controls. In contrast, an eSNP rs4234898 previously identified based on eQTL from the lymphoblastic cell lines of dyslexic children had no chromatin interaction with its target gene SLC2A3 in hippocampus tissues and SLC2A3 expressed higher in the schizophrenia patients than controls. We genotyped the three eSNPs in the READ cohort of 372 cases and 354 controls and discovered only weak associations in rs201605 and rs4234898 with three DD symptoms (p < .05). The lack of associations could be due to low power in READ but could also implicate different etiology of DD in Chinese.
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Affiliation(s)
- Lingfei Liu
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huaiting Gu
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang Hou
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinyan Xie
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Li
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bing Zhu
- Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Jiajia Zhang
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, South Carolina
| | - Wen-Hua Wei
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Ranran Song
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Benítez-Burraco A, Kimura R. Robust Candidates for Language Development and Evolution Are Significantly Dysregulated in the Blood of People With Williams Syndrome. Front Neurosci 2019; 13:258. [PMID: 30971880 PMCID: PMC6444191 DOI: 10.3389/fnins.2019.00258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/05/2019] [Indexed: 01/06/2023] Open
Abstract
Williams syndrome (WS) is a clinical condition, involving cognitive deficits and an uneven language profile, which has been the object of intense inquiry over the last decades. Although WS results from the hemideletion of around two dozen genes in chromosome 7, no gene has yet been probed to account for, or contribute significantly to, the language problems exhibited by the affected people. In this paper we have relied on gene expression profiles in the peripheral blood of WS patients obtained by microarray analysis and show that several robust candidates for language disorders and/or for language evolution in the species, all of them located outside the hemideleted region, are up- or downregulated in the blood of subjects with WS. Most of these genes play a role in the development and function of brain areas involved in language processing, which exhibit structural and functional anomalies in people with this condition. Overall, these genes emerge as robust candidates for language dysfunction in WS.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain
| | - Ryo Kimura
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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28
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Gialluisi A, Andlauer TFM, Mirza-Schreiber N, Moll K, Becker J, Hoffmann P, Ludwig KU, Czamara D, St Pourcain B, Brandler W, Honbolygó F, Tóth D, Csépe V, Huguet G, Morris AP, Hulslander J, Willcutt EG, DeFries JC, Olson RK, Smith SD, Pennington BF, Vaessen A, Maurer U, Lyytinen H, Peyrard-Janvid M, Leppänen PHT, Brandeis D, Bonte M, Stein JF, Talcott JB, Fauchereau F, Wilcke A, Francks C, Bourgeron T, Monaco AP, Ramus F, Landerl K, Kere J, Scerri TS, Paracchini S, Fisher SE, Schumacher J, Nöthen MM, Müller-Myhsok B, Schulte-Körne G. Genome-wide association scan identifies new variants associated with a cognitive predictor of dyslexia. Transl Psychiatry 2019; 9:77. [PMID: 30741946 PMCID: PMC6370792 DOI: 10.1038/s41398-019-0402-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/02/2019] [Indexed: 12/12/2022] Open
Abstract
Developmental dyslexia (DD) is one of the most prevalent learning disorders, with high impact on school and psychosocial development and high comorbidity with conditions like attention-deficit hyperactivity disorder (ADHD), depression, and anxiety. DD is characterized by deficits in different cognitive skills, including word reading, spelling, rapid naming, and phonology. To investigate the genetic basis of DD, we conducted a genome-wide association study (GWAS) of these skills within one of the largest studies available, including nine cohorts of reading-impaired and typically developing children of European ancestry (N = 2562-3468). We observed a genome-wide significant effect (p < 1 × 10-8) on rapid automatized naming of letters (RANlet) for variants on 18q12.2, within MIR924HG (micro-RNA 924 host gene; rs17663182 p = 4.73 × 10-9), and a suggestive association on 8q12.3 within NKAIN3 (encoding a cation transporter; rs16928927, p = 2.25 × 10-8). rs17663182 (18q12.2) also showed genome-wide significant multivariate associations with RAN measures (p = 1.15 × 10-8) and with all the cognitive traits tested (p = 3.07 × 10-8), suggesting (relational) pleiotropic effects of this variant. A polygenic risk score (PRS) analysis revealed significant genetic overlaps of some of the DD-related traits with educational attainment (EDUyears) and ADHD. Reading and spelling abilities were positively associated with EDUyears (p ~ [10-5-10-7]) and negatively associated with ADHD PRS (p ~ [10-8-10-17]). This corroborates a long-standing hypothesis on the partly shared genetic etiology of DD and ADHD, at the genome-wide level. Our findings suggest new candidate DD susceptibility genes and provide new insights into the genetics of dyslexia and its comorbities.
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Affiliation(s)
- Alessandro Gialluisi
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (Sypartially), Munich, Germany
- Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Italy
| | - Till F M Andlauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (Sypartially), Munich, Germany
| | - Nazanin Mirza-Schreiber
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Kristina Moll
- Department of Child and Adolescent Psychiatry, Psychosomatic, and Psychotherapy, Ludwig-Maximilians University, Munich, Germany
| | - Jessica Becker
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - William Brandler
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
| | - Ferenc Honbolygó
- Brain Imaging Centre, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Dénes Tóth
- Brain Imaging Centre, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Valéria Csépe
- Brain Imaging Centre, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Guillaume Huguet
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Andrew P Morris
- Department of Biostatistics, Universiy of Liverpool, Liverpool, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jacqueline Hulslander
- Institute for Behavioral Genetics and Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Erik G Willcutt
- Institute for Behavioral Genetics and Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - John C DeFries
- Institute for Behavioral Genetics and Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Richard K Olson
- Institute for Behavioral Genetics and Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Shelley D Smith
- Developmental Neuroscience Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bruce F Pennington
- Developmental Neuropsychology Lab & Clinic, Department of Psychology, University of Denver, Denver, CO, USA
| | - Anniek Vaessen
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience & Maastricht Brain Imaging Center (M-BIC), Maastricht University, Maastricht, Netherlands
| | - Urs Maurer
- Department of Psychology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Heikki Lyytinen
- Centre for Research on Learning and Teaching, Department of Psychology, University of Jyväskylä, Jyväskylä, Finland
| | | | - Paavo H T Leppänen
- Centre for Research on Learning and Teaching, Department of Psychology, University of Jyväskylä, Jyväskylä, Finland
| | - Daniel Brandeis
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric Hospital, University of Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), Zurich, Switzerland
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Milene Bonte
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience & Maastricht Brain Imaging Center (M-BIC), Maastricht University, Maastricht, Netherlands
| | - John F Stein
- Department of Physiology, University of Oxford, Oxford, UK
| | - Joel B Talcott
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | - Fabien Fauchereau
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Arndt Wilcke
- Cognitive Genetics Unit, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Anthony P Monaco
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Tufts University, Medford, MA, USA
| | - Franck Ramus
- Laboratoire de Sciences Cognitives et Psycholinguistique, Ecole Normale Supérieure, CNRS, EHESS, PSL Research University, Paris, France
| | - Karin Landerl
- Institute of Psychology, University of Graz, Graz, Austria and BioTechMed, Graz, Austria
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Molecular Medicine Program, Biomedicum, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland
- School of Basic and Medical Biosciences, King's College London, London, UK
| | - Thomas S Scerri
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- The Walter and Eliza Hall Institute of Medical Research & Melbourne University, Melbourne, Australia
| | | | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
| | - Johannes Schumacher
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Bertram Müller-Myhsok
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany.
- Munich Cluster for Systems Neurology (Sypartially), Munich, Germany.
- Institute of Translational Medicine, University of Liverpool, Liverpool, UK.
| | - Gerd Schulte-Körne
- Department of Child and Adolescent Psychiatry, Psychosomatic, and Psychotherapy, Ludwig-Maximilians University, Munich, Germany.
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29
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Pérez RF, Santamarina P, Tejedor JR, Urdinguio RG, Álvarez-Pitti J, Redon P, Fernández AF, Fraga MF, Lurbe E. Longitudinal genome-wide DNA methylation analysis uncovers persistent early-life DNA methylation changes. J Transl Med 2019; 17:15. [PMID: 30626398 PMCID: PMC6327427 DOI: 10.1186/s12967-018-1751-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 01/08/2023] Open
Abstract
Background Early life is a period of drastic epigenetic remodeling in which the epigenome is especially sensitive to extrinsic and intrinsic influence. However, the epigenome-wide dynamics of the DNA methylation changes that occur during this period have not been sufficiently characterized in longitudinal studies. Methods To this end, we studied the DNA methylation status of more than 750,000 CpG sites using Illumina MethylationEPIC arrays on 33 paired blood samples from 11 subjects at birth and at 5 and 10 years of age, then characterized the chromatin context associated with these loci by integrating our data with histone, chromatin-state and enhancer-element external datasets, and, finally, validated our results through bisulfite pyrosequencing in two independent longitudinal cohorts of 18 additional subjects. Results We found abundant DNA methylation changes (110,726 CpG sites) during the first lustrum of life, while far fewer alterations were observed in the subsequent 5 years (460 CpG sites). However, our analysis revealed persistent DNA methylation changes at 240 CpG sites, indicating that there are genomic locations of considerable epigenetic change beyond immediate birth. The chromatin context of hypermethylation changes was associated with repressive genomic locations and genes with developmental and cell signaling functions, while hypomethylation changes were linked to enhancer regions and genes with immunological and mRNA and protein metabolism functions. Significantly, our results show that genes that suffer simultaneous hyper- and hypomethylation are functionally distinct from exclusively hyper- or hypomethylated genes, and that enhancer-associated methylation is different in hyper- and hypomethylation scenarios, with hypomethylation being more associated to epigenetic changes at blood tissue-specific enhancer elements. Conclusions These data show that epigenetic remodeling is dramatically reduced after the first 5 years of life. However, there are certain loci which continue to manifest DNA methylation changes, pointing towards a possible functionality beyond early development. Furthermore, our results deepen the understanding of the genomic context associated to hyper- or hypomethylation alterations during time, suggesting that hypomethylation of blood tissue-specific enhancer elements could be of importance in the establishment of functional states in blood tissue during early-life. Electronic supplementary material The online version of this article (10.1186/s12967-018-1751-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raúl F Pérez
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain.,Nanomedicine Group, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, 33940, Oviedo, Asturias, Spain
| | - Pablo Santamarina
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain.,Nanomedicine Group, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, 33940, Oviedo, Asturias, Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Rocío G Urdinguio
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Julio Álvarez-Pitti
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, 46014, Valencia, Spain.,Centros de Investigación Biomédica en Red de Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain
| | - Pau Redon
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, 46014, Valencia, Spain.,Centros de Investigación Biomédica en Red de Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain
| | - Agustín F Fernández
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Mario F Fraga
- Nanomedicine Group, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, 33940, Oviedo, Asturias, Spain.
| | - Empar Lurbe
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, 46014, Valencia, Spain. .,Centros de Investigación Biomédica en Red de Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain.
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30
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Vevera J, Zarrei M, Hartmannová H, Jedličková I, Mušálková D, Přistoupilová A, Oliveriusová P, Trešlová H, Nosková L, Hodaňová K, Stránecký V, Jiřička V, Preiss M, Příhodová K, Šaligová J, Wei J, Woodbury-Smith M, Bleyer AJ, Scherer SW, Kmoch S. Rare copy number variation in extremely impulsively violent males. Genes, Brain and Behavior 2018; 18:e12536. [DOI: 10.1111/gbb.12536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Jan Vevera
- Department of Psychiatry; Faculty of Medicine and University Hospital in Pilsen, Charles University; Prague Czech Republic
- Department of Psychiatry, First Faculty of Medicine; Charles University and General University Hospital in Prague; Prague Czech Republic
- Institute for Postgraduate Medical Education; Prague Czech Republic
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
| | - Mehdi Zarrei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
| | - Hana Hartmannová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Ivana Jedličková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Dita Mušálková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Anna Přistoupilová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Petra Oliveriusová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Helena Trešlová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Lenka Nosková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Václav Jiřička
- Prison Service of the Czech Republic, Directorate General; Department of Psychology; Prague Czech Republic
| | - Marek Preiss
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
- Psychology Department; University of New York in Prague; Prague Czech Republic
| | - Kateřina Příhodová
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
| | - Jana Šaligová
- Children's Faculty Hospital; Department of Pediatrics and Adolescent Medicine; Kosice Slovakia
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine of Pavel Jozef Šafárik University Kosice; Kosice Slovakia
| | - John Wei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
| | - Marc Woodbury-Smith
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
- Institute of Neuroscience, Newcastle University, Sir James Spence Institute, Royal Victoria Infirmary; Newcastle upon Tyne UK
| | - Anthony J. Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
- Section on Nephrology, Wake Forest School of Medicine; Medical Center Blvd.; Winston-Salem North Carolina USA
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
- Department of Molecular Genetics and McLaughlin Centre; University of Toronto; Toronto Ontario Canada
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
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31
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Guidi LG, Velayos‐Baeza A, Martinez‐Garay I, Monaco AP, Paracchini S, Bishop DVM, Molnár Z. The neuronal migration hypothesis of dyslexia: A critical evaluation 30 years on. Eur J Neurosci 2018; 48:3212-3233. [PMID: 30218584 PMCID: PMC6282621 DOI: 10.1111/ejn.14149] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/06/2018] [Accepted: 08/13/2018] [Indexed: 12/29/2022]
Abstract
The capacity for language is one of the key features underlying the complexity of human cognition and its evolution. However, little is known about the neurobiological mechanisms that mediate normal or impaired linguistic ability. For developmental dyslexia, early postmortem studies conducted in the 1980s linked the disorder to subtle defects in the migration of neurons in the developing neocortex. These early studies were reinforced by human genetic analyses that identified dyslexia susceptibility genes and subsequent evidence of their involvement in neuronal migration. In this review, we examine recent experimental evidence that does not support the link between dyslexia and neuronal migration. We critically evaluate gene function studies conducted in rodent models and draw attention to the lack of robust evidence from histopathological and imaging studies in humans. Our review suggests that the neuronal migration hypothesis of dyslexia should be reconsidered, and the neurobiological basis of dyslexia should be approached with a fresh start.
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Affiliation(s)
- Luiz G. Guidi
- Department of Physiology, Anatomy, and GeneticsUniversity of OxfordOxfordUK
- Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Antonio Velayos‐Baeza
- Department of Physiology, Anatomy, and GeneticsUniversity of OxfordOxfordUK
- Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Isabel Martinez‐Garay
- Department of Physiology, Anatomy, and GeneticsUniversity of OxfordOxfordUK
- Division of NeuroscienceSchool of BiosciencesCardiff UniversityCardiffUK
| | | | | | | | - Zoltán Molnár
- Department of Physiology, Anatomy, and GeneticsUniversity of OxfordOxfordUK
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32
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Rios DM, Correia Rios M, Bandeira ID, Queiros Campbell F, de Carvalho Vaz D, Lucena R. Impact of Transcranial Direct Current Stimulation on Reading Skills of Children and Adolescents With Dyslexia. Child Neurol Open 2018; 5:2329048X18798255. [PMID: 30306098 PMCID: PMC6174647 DOI: 10.1177/2329048x18798255] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 07/26/2018] [Accepted: 08/10/2018] [Indexed: 12/27/2022] Open
Abstract
Introduction: Rehabilitation techniques have been used to facilitate reading acquisition in dyslexia. However, many individuals continue to present academic impairment throughout life. New intervention strategies are necessary to further help this population. Objectives: Assess the impact of transcranial direct current stimulation on reading skills in children and adolescents with dyslexia. Methods: The study was conducted with one-group pretest–posttest. Participants received 2 mA transcranial direct current stimulation during 30 minutes for 5 consecutive days. Reading performance was measured by a group of tasks (identification and reading of letters, syllables, words, nonwords, and text). Results: A significant increase in the number of correct answers for nonwords and text tasks was observed after transcranial direct current stimulation (P = .035 and P = .012, respectively). Conclusion: The transcranial direct current stimulation seems to be a promising tool for the treatment of reading problems in dyslexia. Future studies are necessary to confirm the effects of transcranial direct current stimulation and to establish optimal intervention protocol in this population.
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Affiliation(s)
- Débora Medeiros Rios
- Department of Neuroscience and Mental Health, Medical School of Bahia, Federal University of Bahia, Salvador, Brazil
| | | | - Igor Dórea Bandeira
- Department of Neuroscience and Mental Health, Medical School of Bahia, Federal University of Bahia, Salvador, Brazil
| | - Fernanda Queiros Campbell
- Department of Biomorphology, Health Sciences Institute, Federal University of Bahia, Salvador, Brazil
| | - Daniel de Carvalho Vaz
- Department of Neuroscience and Mental Health, Medical School of Bahia, Federal University of Bahia, Salvador, Brazil
| | - Rita Lucena
- Department of Neuroscience and Mental Health, Medical School of Bahia, Federal University of Bahia, Salvador, Brazil
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Tylee DS, Sun J, Hess JL, Tahir MA, Sharma E, Malik R, Worrall BB, Levine AJ, Martinson JJ, Nejentsev S, Speed D, Fischer A, Mick E, Walker BR, Crawford A, Grant SF, Polychronakos C, Bradfield JP, Sleiman PMA, Hakonarson H, Ellinghaus E, Elder JT, Tsoi LC, Trembath RC, Barker JN, Franke A, Dehghan A, Faraone SV, Glatt. SJ. Genetic correlations among psychiatric and immune-related phenotypes based on genome-wide association data. Am J Med Genet B Neuropsychiatr Genet 2018; 177:641-657. [PMID: 30325587 PMCID: PMC6230304 DOI: 10.1002/ajmg.b.32652] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 02/21/2018] [Accepted: 05/22/2018] [Indexed: 12/18/2022]
Abstract
Individuals with psychiatric disorders have elevated rates of autoimmune comorbidity and altered immune signaling. It is unclear whether these altered immunological states have a shared genetic basis with those psychiatric disorders. The present study sought to use existing summary-level data from previous genome-wide association studies to determine if commonly varying single nucleotide polymorphisms are shared between psychiatric and immune-related phenotypes. We estimated heritability and examined pair-wise genetic correlations using the linkage disequilibrium score regression (LDSC) and heritability estimation from summary statistics methods. Using LDSC, we observed significant genetic correlations between immune-related disorders and several psychiatric disorders, including anorexia nervosa, attention deficit-hyperactivity disorder, bipolar disorder, major depression, obsessive compulsive disorder, schizophrenia, smoking behavior, and Tourette syndrome. Loci significantly mediating genetic correlations were identified for schizophrenia when analytically paired with Crohn's disease, primary biliary cirrhosis, systemic lupus erythematosus, and ulcerative colitis. We report significantly correlated loci and highlight those containing genome-wide associations and candidate genes for respective disorders. We also used the LDSC method to characterize genetic correlations among the immune-related phenotypes. We discuss our findings in the context of relevant genetic and epidemiological literature, as well as the limitations and caveats of the study.
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Affiliation(s)
- Daniel S. Tylee
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Jiayin Sun
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Jonathan L. Hess
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Muhammad A. Tahir
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Esha Sharma
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Rainer Malik
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Bradford B. Worrall
- Departments of Neurology and Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, U.S.A
| | - Andrew J. Levine
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, U.S.A
| | - Jeremy J. Martinson
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, PA, U.S.A
| | | | - Doug Speed
- Aarhus Institute for Advanced Studies and University College London, London, U.K
| | - Annegret Fischer
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Eric Mick
- Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, U.S.A
| | - Brian R. Walker
- BHF Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, U.K
| | - Andrew Crawford
- School of Social and Community Medicine, MRC Integrated Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Center for Applied Genomics, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, U.S.A
| | - Struan F.A. Grant
- Center for Applied Genomics, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, U.S.A
- Division of Endocrinology and Diabetes, The Children’s Hospital of Philadelphia, Philadelphia, PA, U.S.A
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Constantin Polychronakos
- Endocrine Genetics Laboratory, Department of Pediatrics and the Child Health Program of the Research Institute, McGill University Health Centre, Montreal, Quebec, Canada
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, U.S.A
- Quantinuum Research LLC, San Diego, CA, U.S.A
| | - Patrick M. A. Sleiman
- Center for Applied Genomics, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, U.S.A
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Hakon Hakonarson
- Center for Applied Genomics, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, U.S.A
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - James T. Elder
- Department of Dermatology, Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lam C. Tsoi
- Department of Dermatology, Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Richard C. Trembath
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Jonathan N. Barker
- Department of Biostatistics and Epidemiology, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Abbas Dehghan
- Department of Biostatistics and Epidemiology, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London
| | | | | | - Stephen V. Faraone
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
- K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Stephen J. Glatt.
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
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Wen C, Mehta CM, Tan H, Zhang H. Whole genome association study of brain-wide imaging phenotypes: A study of the ping cohort. Genet Epidemiol 2018; 42:265-275. [PMID: 29411414 PMCID: PMC5851842 DOI: 10.1002/gepi.22111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 11/08/2017] [Accepted: 12/07/2017] [Indexed: 02/05/2023]
Abstract
Neuropsychological disorders have a biological basis rooted in brain function, and neuroimaging data are expected to better illuminate the complex genetic basis of neuropsychological disorders. Because they are biological measures, neuroimaging data avoid biases arising from clinical diagnostic criteria that are subject to human understanding and interpretation. A challenge with analyzing neuroimaging data is their high dimensionality and complex spatial relationships. To tackle this challenge, we introduced a novel distance covariance tests that can assess the association between genetic markers and multivariate diffusion tensor imaging measurements, and analyzed a genome-wide association study (GWAS) dataset collected by the Pediatric Imaging, Neurocognition, and Genetics (PING) study. We also considered existing approaches as comparisons. Our results showed that, after correcting for multiplicity, distance covariance tests of the multivariate phenotype yield significantly greater power at detecting genetic markers affecting brain structure than standard mass univariate GWAS of individual neuroimaging biomarkers. Our results underscore the usefulness of utilizing the distance covariance to incorporate neuroimaging data in GWAS.
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Affiliation(s)
- Canhong Wen
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
- Department of Statistics and Finance, School of Management, University of Science and Technology of China, Hefei, China
- Department of Statistical Science, School of Mathematics, Sun Yat-Sen University, Guangzhou, China
| | - Chintan M. Mehta
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Haizhu Tan
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
- Department of Physics and Computer Applications, Shantou University Medical College, Shantou, China
| | - Heping Zhang
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
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35
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McMahon AW, Kapcala LP, Sheridan PH. Workshop on evaluation of pediatric long-term neurocognitive development and medical products. Pharmacoepidemiol Drug Saf 2017; 26:1428-1430. [PMID: 28924994 DOI: 10.1002/pds.4306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 06/13/2017] [Accepted: 08/15/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Ann W McMahon
- Office of Pediatric Therapeutics, Food and Drug Administration, Silver Spring, MD, USA
| | - Leonard P Kapcala
- Division of Neurology Products, Food and Drug Administration, Silver Spring, MD, USA
| | - Philip H Sheridan
- Division of Neurology Products, Food and Drug Administration, Silver Spring, MD, USA
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36
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Deriziotis P, Fisher SE. Speech and Language: Translating the Genome. Trends Genet 2017; 33:642-656. [DOI: 10.1016/j.tig.2017.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 01/30/2023]
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Einarsdottir E, Peyrard-Janvid M, Darki F, Tuulari JJ, Merisaari H, Karlsson L, Scheinin NM, Saunavaara J, Parkkola R, Kantojärvi K, Ämmälä AJ, Yiu-Lin Yu N, Matsson H, Nopola-Hemmi J, Karlsson H, Paunio T, Klingberg T, Leinonen E, Kere J. Identification of NCAN as a candidate gene for developmental dyslexia. Sci Rep 2017; 7:9294. [PMID: 28839234 DOI: 10.1038/s41598-017-10175-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 08/04/2017] [Indexed: 01/22/2023] Open
Abstract
A whole-genome linkage analysis in a Finnish pedigree of eight cases with developmental dyslexia (DD) revealed several regions shared by the affected individuals. Analysis of coding variants from two affected individuals identified rs146011974G > A (Ala1039Thr), a rare variant within the NCAN gene co-segregating with DD in the pedigree. This variant prompted us to consider this gene as a putative candidate for DD. The RNA expression pattern of the NCAN gene in human tissues was highly correlated (R > 0.8) with that of the previously suggested DD susceptibility genes KIAA0319, CTNND2, CNTNAP2 and GRIN2B. We investigated the association of common variation in NCAN to brain structures in two data sets: young adults (Brainchild study, Sweden) and infants (FinnBrain study, Finland). In young adults, we found associations between a common genetic variant in NCAN, rs1064395, and white matter volume in the left and right temporoparietal as well as the left inferior frontal brain regions. In infants, this same variant was found to be associated with cingulate and prefrontal grey matter volumes. Our results suggest NCAN as a new candidate gene for DD and indicate that NCAN variants affect brain structure.
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38
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Maciukiewicz M, Marshe VS, Tiwari AK, Fonseka TM, Freeman N, Kennedy JL, Rotzinger S, Foster JA, Kennedy SH, Müller DJ. Genome-wide association studies of placebo and duloxetine response in major depressive disorder. Pharmacogenomics J 2017; 18:406-412. [PMID: 28696415 DOI: 10.1038/tpj.2017.29] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 03/01/2017] [Accepted: 03/16/2017] [Indexed: 12/28/2022]
Abstract
We investigated variants associated with treatment response in depressed patients treated with either the antidepressant duloxetine or placebo using a genome-wide approach. Our sample (N=391) included individuals aged 18-75 years, diagnosed with major depressive disorder and treated with either duloxetine or placebo for up to 8 weeks. We conducted genome-wide associations for treatment response as operationalized by percentage change in Montgomery-Åsberg Depression Rating Scale score from baseline, as well as mixed models analyses across five time points. In the placebo-treated subsample (N=205), we observed a genome-wide association with rs76767803 (β=0.69, P=1.25 × 10-8) upstream of STAC1. STAC1 rs76767803 was also associated with response using mixed model analysis (χ2=3.95; P=0.001). In the duloxetine-treated subsample (N=186), we observed suggestive associations with ZNF385D (rs4261893; β=-0.46, P=1.55 × 10-5), NCAM1 (rs2303377; β=0.45, P=1.76 × 10-5) and MLL5 (rs117986340; β=0.91, P=3.04 × 10-5). Our findings suggest that a variant upstream of STAC1 is associated with placebo response, which might have implications for treatment optimization, clinical trial design and drug development.
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Affiliation(s)
- M Maciukiewicz
- Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - V S Marshe
- Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - A K Tiwari
- Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - T M Fonseka
- Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Department of Psychiatry, University Health Network, Toronto, ON, Canada.,Department of Psychiatry, St. Michael's Hospital, Toronto, ON, Canada
| | - N Freeman
- Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - J L Kennedy
- Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - S Rotzinger
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University Health Network, Toronto, ON, Canada
| | - J A Foster
- Department of Psychiatry and Behavioral Neurosciences, McMaster University, Hamilton, ON, Canada
| | - S H Kennedy
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University Health Network, Toronto, ON, Canada.,Department of Psychiatry, St. Michael's Hospital, Toronto, ON, Canada
| | - D J Müller
- Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
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39
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Selzam S, Dale PS, Wagner RK, DeFries JC, Cederlöf M, O’Reilly PF, Krapohl E, Plomin R. Genome-Wide Polygenic Scores Predict Reading Performance Throughout the School Years. Sci Stud Read 2017; 21:334-349. [PMID: 28706435 PMCID: PMC5490720 DOI: 10.1080/10888438.2017.1299152] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
It is now possible to create individual-specific genetic scores, called genome-wide polygenic scores (GPS). We used a GPS for years of education (EduYears) to predict reading performance assessed at UK National Curriculum Key Stages 1 (age 7), 2 (age 12) and 3 (age 14) and on reading tests administered at ages 7 and 12 in a UK sample of 5,825 unrelated individuals. EduYears GPS accounts for up to 5% of the variance in reading performance at age 14. GPS predictions remained significant after accounting for general cognitive ability and family socioeconomic status. Reading performance of children in the lowest and highest 12.5% of the EduYears GPS distribution differed by a mean growth in reading ability of approximately two school years. It seems certain that polygenic scores will be used to predict strengths and weaknesses in education.
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Hull EE, Montgomery MR, Leyva KJ. Epigenetic Regulation of the Biosynthesis & Enzymatic Modification of Heparan Sulfate Proteoglycans: Implications for Tumorigenesis and Cancer Biomarkers. Int J Mol Sci 2017; 18:E1361. [PMID: 28672878 DOI: 10.3390/ijms18071361] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/05/2017] [Accepted: 06/22/2017] [Indexed: 02/06/2023] Open
Abstract
Emerging evidence suggests that the enzymes in the biosynthetic pathway for the synthesis of heparan sulfate moieties of heparan sulfate proteoglycans (HSPGs) are epigenetically regulated at many levels. As the exact composition of the heparan sulfate portion of the resulting HSPG molecules is critical to the broad spectrum of biological processes involved in oncogenesis, the epigenetic regulation of heparan sulfate biosynthesis has far-reaching effects on many cellular activities related to cancer progression. Given the current focus on developing new anti-cancer therapeutics focused on epigenetic targets, it is important to understand the effects that these emerging therapeutics may have on the synthesis of HSPGs as alterations in HSPG composition may have profound and unanticipated effects. As an introduction, this review will briefly summarize the variety of important roles which HSPGs play in a wide-spectrum of cancer-related cellular and physiological functions and then describe the biosynthesis of the heparan sulfate chains of HSPGs, including how alterations observed in cancer cells serve as potential biomarkers. This review will then focus on detailing the multiple levels of epigenetic regulation of the enzymes in the heparan sulfate synthesis pathway with a particular focus on regulation by miRNA and effects of epigenetic therapies on HSPGs. We will also explore the use of lectins to detect differences in heparan sulfate composition and preview their potential diagnostic and prognostic use in the clinic.
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Carrion-Castillo A, van Bergen E, Vino A, van Zuijen T, de Jong PF, Francks C, Fisher SE. Evaluation of results from genome-wide studies of language and reading in a novel independent dataset. Genes Brain Behav 2017; 15:531-41. [PMID: 27198479 DOI: 10.1111/gbb.12299] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/17/2016] [Accepted: 05/17/2016] [Indexed: 01/05/2023]
Abstract
Recent genome-wide association scans (GWAS) for reading and language abilities have pin-pointed promising new candidate loci. However, the potential contributions of these loci remain to be validated. In this study, we tested 17 of the most significantly associated single nucleotide polymorphisms (SNPs) from these GWAS studies (P < 10(-6) in the original studies) in a new independent population dataset from the Netherlands: known as Familial Influences on Literacy Abilities. This dataset comprised 483 children from 307 nuclear families and 505 adults (including parents of participating children), and provided adequate statistical power to detect the effects that were previously reported. The following measures of reading and language performance were collected: word reading fluency, nonword reading fluency, phonological awareness and rapid automatized naming. Two SNPs (rs12636438 and rs7187223) were associated with performance in multivariate and univariate testing, but these did not remain significant after correction for multiple testing. Another SNP (rs482700) was only nominally associated in the multivariate test. For the rest of the SNPs, we did not find supportive evidence of association. The findings may reflect differences between our study and the previous investigations with respect to the language of testing, the exact tests used and the recruitment criteria. Alternatively, most of the prior reported associations may have been false positives. A larger scale GWAS meta-analysis than those previously performed will likely be required to obtain robust insights into the genomic architecture underlying reading and language.
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Affiliation(s)
- A Carrion-Castillo
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - E van Bergen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.,Department of Experimental Psychology, University of Oxford, Oxford, UK
| | - A Vino
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - T van Zuijen
- Research Institute of Child Development and Education, University of Amsterdam, Amsterdam, the Netherlands
| | - P F de Jong
- Research Institute of Child Development and Education, University of Amsterdam, Amsterdam, the Netherlands
| | - C Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - S E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
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42
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Muntané G, Santpere G, Verendeev A, Seeley WW, Jacobs B, Hopkins WD, Navarro A, Sherwood CC. Interhemispheric gene expression differences in the cerebral cortex of humans and macaque monkeys. Brain Struct Funct 2017; 222:3241-3254. [PMID: 28317062 DOI: 10.1007/s00429-017-1401-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/05/2017] [Indexed: 11/25/2022]
Abstract
Handedness and language are two well-studied examples of asymmetrical brain function in humans. Approximately 90% of humans exhibit a right-hand preference, and the vast majority shows left-hemisphere dominance for language function. Although genetic models of human handedness and language have been proposed, the actual gene expression differences between cerebral hemispheres in humans remain to be fully defined. In the present study, gene expression profiles were examined in both hemispheres of three cortical regions involved in handedness and language in humans and their homologues in rhesus macaques: ventrolateral prefrontal cortex, posterior superior temporal cortex (STC), and primary motor cortex. Although the overall pattern of gene expression was very similar between hemispheres in both humans and macaques, weighted gene correlation network analysis revealed gene co-expression modules associated with hemisphere, which are different among the three cortical regions examined. Notably, a receptor-enriched gene module in STC was particularly associated with hemisphere and showed different expression levels between hemispheres only in humans.
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Affiliation(s)
- Gerard Muntané
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, 20052, USA.
- Institut Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, 08003, Barcelona, Spain.
| | - Gabriel Santpere
- Institut Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, 08003, Barcelona, Spain
| | - Andrey Verendeev
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, 20052, USA
| | - William W Seeley
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, 94158, USA
| | - Bob Jacobs
- Laboratory of Quantitative Neuromorphology, Neuroscience Program, Colorado College, Colorado Springs, CO, 80903, USA
| | - William D Hopkins
- Neuroscience Institute and the Language Research Center, Georgia State University, Atlanta, GA, 30302, USA
| | - Arcadi Navarro
- Institut Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, 08003, Barcelona, Spain
| | - Chet C Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, 20052, USA
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43
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Eicher JD, Montgomery AM, Akshoomoff N, Amaral DG, Bloss CS, Libiger O, Schork NJ, Darst BF, Casey BJ, Chang L, Ernst T, Frazier J, Kaufmann WE, Keating B, Kenet T, Kennedy D, Mostofsky S, Murray SS, Sowell ER, Bartsch H, Kuperman JM, Brown TT, Hagler DJ, Dale AM, Jernigan TL, Gruen JR. Dyslexia and language impairment associated genetic markers influence cortical thickness and white matter in typically developing children. Brain Imaging Behav 2016; 10:272-82. [PMID: 25953057 PMCID: PMC4639472 DOI: 10.1007/s11682-015-9392-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Dyslexia and language impairment (LI) are complex traits with substantial genetic components. We recently completed an association scan of the DYX2 locus, where we observed associations of markers in DCDC2, KIAA0319, ACOT13, and FAM65B with reading-, language-, and IQ-related traits. Additionally, the effects of reading-associated DYX3 markers were recently characterized using structural neuroimaging techniques. Here, we assessed the neuroimaging implications of associated DYX2 and DYX3 markers, using cortical volume, cortical thickness, and fractional anisotropy. To accomplish this, we examined eight DYX2 and three DYX3 markers in 332 subjects in the Pediatrics Imaging Neurocognition Genetics study. Imaging-genetic associations were examined by multiple linear regression, testing for influence of genotype on neuroimaging. Markers in DYX2 genes KIAA0319 and FAM65B were associated with cortical thickness in the left orbitofrontal region and global fractional anisotropy, respectively. KIAA0319 and ACOT13 were suggestively associated with overall fractional anisotropy and left pars opercularis cortical thickness, respectively. DYX3 markers showed suggestive associations with cortical thickness and volume measures in temporal regions. Notably, we did not replicate association of DYX3 markers with hippocampal measures. In summary, we performed a neuroimaging follow-up of reading-, language-, and IQ-associated DYX2 and DYX3 markers. DYX2 associations with cortical thickness may reflect variations in their role in neuronal migration. Furthermore, our findings complement gene expression and imaging studies implicating DYX3 markers in temporal regions. These studies offer insight into where and how DYX2 and DYX3 risk variants may influence neuroimaging traits. Future studies should further connect the pathways to risk variants associated with neuroimaging/neurocognitive outcomes.
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Affiliation(s)
- John D Eicher
- Department of Genetics, Yale University, New Haven, CT, 06520, USA
| | - Angela M Montgomery
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Natacha Akshoomoff
- Center for Human Development, University of California, La Jolla, San Diego, CA, 92037, USA
- Department of Psychiatry, University of California, La Jolla, San Diego, CA, 92037, USA
| | - David G Amaral
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA, 95817, USA
| | - Cinnamon S Bloss
- Scripps Genomic Medicine, Scripps Health, Scripps Translational Science Institute, La Jolla, CA, 92037, USA
| | - Ondrej Libiger
- Scripps Genomic Medicine, Scripps Health, Scripps Translational Science Institute, La Jolla, CA, 92037, USA
| | - Nicholas J Schork
- Scripps Genomic Medicine, Scripps Health, Scripps Translational Science Institute, La Jolla, CA, 92037, USA
| | - Burcu F Darst
- Scripps Genomic Medicine, Scripps Health, Scripps Translational Science Institute, La Jolla, CA, 92037, USA
| | - B J Casey
- Sackler Institute for Developmental Psychobiology, Weil Cornell Medical College, New York, NY, 10065, USA
| | - Linda Chang
- Department of Medicine, Queen's Medical Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Thomas Ernst
- Department of Medicine, Queen's Medical Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Jean Frazier
- Department of Psychiatry, University of Massachusetts Medical School, Boston, MA, 01655, USA
| | - Walter E Kaufmann
- Kennedy Krieger Institute, 707 N. Broadway, Baltimore, MD, 21205, USA
- Department of Neurology, Harvard Medical School, Children's Hospital Boston, Boston, MA, 02115, USA
| | - Brian Keating
- Department of Medicine, Queen's Medical Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Tal Kenet
- Department of Neurology and Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, 02129, USA
| | - David Kennedy
- Department of Psychiatry, University of Massachusetts Medical School, Boston, MA, 01655, USA
| | - Stewart Mostofsky
- Kennedy Krieger Institute, 707 N. Broadway, Baltimore, MD, 21205, USA
| | - Sarah S Murray
- Scripps Genomic Medicine, Scripps Health, Scripps Translational Science Institute, La Jolla, CA, 92037, USA
| | - Elizabeth R Sowell
- Department of Pediatrics, University of Southern California, Los Angeles, CA, 90027, USA
- Developmental Cognitive Neuroimaging Laboratory Children's Hospital, Los Angeles, CA, 90027, USA
| | - Hauke Bartsch
- Multimodal Imaging Laboratory, University of California, La Jolla, San Diego, CA, 92037, USA
| | - Joshua M Kuperman
- Multimodal Imaging Laboratory, University of California, La Jolla, San Diego, CA, 92037, USA
- Department of Neurosciences, University of California, La Jolla, San Diego, CA, 92037, USA
| | - Timothy T Brown
- Center for Human Development, University of California, La Jolla, San Diego, CA, 92037, USA
- Multimodal Imaging Laboratory, University of California, La Jolla, San Diego, CA, 92037, USA
- Department of Neurosciences, University of California, La Jolla, San Diego, CA, 92037, USA
| | - Donald J Hagler
- Multimodal Imaging Laboratory, University of California, La Jolla, San Diego, CA, 92037, USA
- Radiology University of California, La Jolla, San Diego, CA, 92037, USA
| | - Anders M Dale
- Department of Psychiatry, University of California, La Jolla, San Diego, CA, 92037, USA
- Multimodal Imaging Laboratory, University of California, La Jolla, San Diego, CA, 92037, USA
- Department of Neurosciences, University of California, La Jolla, San Diego, CA, 92037, USA
- Radiology University of California, La Jolla, San Diego, CA, 92037, USA
- Cognitive Science University of California, La Jolla, San Diego, CA, 92037, USA
| | - Terry L Jernigan
- Center for Human Development, University of California, La Jolla, San Diego, CA, 92037, USA
- Department of Psychiatry, University of California, La Jolla, San Diego, CA, 92037, USA
- Radiology University of California, La Jolla, San Diego, CA, 92037, USA
- Cognitive Science University of California, La Jolla, San Diego, CA, 92037, USA
| | - Jeffrey R Gruen
- Department of Genetics, Yale University, New Haven, CT, 06520, USA.
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Department of Investigative, School of Medicine, Medicine Yale University, New Haven, CT, 06520, USA.
- Department of Pediatrics, Genetics, and Investigative Medicine, Yale Child Health Research Center, 464 Congress Avenue, New Haven, CT, 06520-8081, USA.
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44
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Kornilov SA, Lebedeva TV, Zhukova MA, Prikhoda NA, Korotaeva IV, Koposov RA, Hart L, Reich J, Grigorenko EL. Language development in rural and urban Russian-speaking children with and without developmental language disorder. Learn Individ Differ 2016; 46:45-53. [PMID: 27346924 DOI: 10.1016/j.lindif.2015.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Using a newly developed Assessment of the Development of Russian Language (ORRIA), we investigated differences in language development between rural vs. urban Russian-speaking children (n = 100 with a mean age of 6.75) subdivided into groups with and without developmental language disorders. Using classical test theory and item response theory approaches, we found that while ORRIA displayed overall satisfactory psychometric properties, several of its items showed differential item functioning favoring rural children, and several others favoring urban children. After the removal of these items, rural children significantly underperformed on ORRIA compared to urban children. The urbanization factor did not significantly interact with language group. We discuss the latter finding in the context of the multiple additive risk factors for language development and emphasize the need for future studies of the mechanisms that underlie these influences and the implications of these findings for our understanding of the etiological architecture of children's language development.
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Affiliation(s)
- Sergey A Kornilov
- Yale University, New Haven, CT, USA; Haskins Laboratories, New Haven, CT, USA; Saint-Petersburg State University, Saint-Petersburg, Russia; Moscow State University, Moscow, Russia
| | - Tatiana V Lebedeva
- City Center for Psychological, Medical, and Social Services, Moscow, Russia; Moscow City University for Psychology and Education, Moscow, Russia
| | | | | | | | | | | | - Jodi Reich
- Yale University, New Haven, CT, USA; Temple University, Philadelphia, PA, USA
| | - Elena L Grigorenko
- Yale University, New Haven, CT, USA; Haskins Laboratories, New Haven, CT, USA; Saint-Petersburg State University, Saint-Petersburg, Russia; Moscow City University for Psychology and Education, Moscow, Russia
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45
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Solso S, Xu R, Proudfoot J, Hagler DJ, Campbell K, Venkatraman V, Barnes CC, Ahrens-Barbeau C, Pierce K, Dale A, Eyler L, Courchesne E. Diffusion Tensor Imaging Provides Evidence of Possible Axonal Overconnectivity in Frontal Lobes in Autism Spectrum Disorder Toddlers. Biol Psychiatry 2016; 79:676-84. [PMID: 26300272 PMCID: PMC4699869 DOI: 10.1016/j.biopsych.2015.06.029] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 12/31/2022]
Abstract
BACKGROUND Theories of brain abnormality in autism spectrum disorder (ASD) have focused on underconnectivity as an explanation for social, language, and behavioral deficits but are based mainly on studies of older autistic children and adults. METHODS In 94 ASD and typical toddlers ages 1 to 4 years, we examined the microstructure (indexed by fractional anisotropy) and volume of axon pathways using in vivo diffusion tensor imaging of fronto-frontal, fronto-temporal, fronto-striatal, and fronto-amygdala axon pathways, as well as posterior contrast tracts. Differences between ASD and typical toddlers in the nature of the relationship of age to these measures were tested. RESULTS Frontal tracts in ASD toddlers displayed abnormal age-related changes with greater fractional anisotropy and volume than normal at younger ages but an overall slower than typical apparent rate of continued development across the span of years. Posterior cortical contrast tracts had few significant abnormalities. CONCLUSIONS Frontal fiber tracts displayed deviant early development and age-related changes that could underlie impaired brain functioning and impact social and communication behaviors in ASD.
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Affiliation(s)
- Stephanie Solso
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Ronghui Xu
- CTRI, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - James Proudfoot
- CTRI, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Donald J. Hagler
- Department of Radiology, Multimodal Imaging Laboratory, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Kathleen Campbell
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Vijay Venkatraman
- Department of Radiology, Multimodal Imaging Laboratory, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Cynthia Carter Barnes
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Clelia Ahrens-Barbeau
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Karen Pierce
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Anders Dale
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla, CA 92093,Department of Radiology, Multimodal Imaging Laboratory, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Lisa Eyler
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla, CA 92093,Department of Psychiatry, School of Medicine, University of California San Diego, La Jolla, CA 92093,Desert-Pacific Mental Illness Research, Education and Clinical Center, VA San Diego Healthcare System, San Diego, CA 92161
| | - Eric Courchesne
- Department of Neuroscience, School of Medicine, University of California San Diego, La Jolla.
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46
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Mueller KL, Murray JC, Michaelson JJ, Christiansen MH, Reilly S, Tomblin JB. Common Genetic Variants in FOXP2 Are Not Associated with Individual Differences in Language Development. PLoS One 2016; 11:e0152576. [PMID: 27064276 PMCID: PMC4827837 DOI: 10.1371/journal.pone.0152576] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 03/16/2016] [Indexed: 02/07/2023] Open
Abstract
Much of our current knowledge regarding the association of FOXP2 with speech and language development comes from singleton and small family studies where a small number of rare variants have been identified. However, neither genome-wide nor gene-specific studies have provided evidence that common polymorphisms in the gene contribute to individual differences in language development in the general population. One explanation for this inconsistency is that previous studies have been limited to relatively small samples of individuals with low language abilities, using low density gene coverage. The current study examined the association between common variants in FOXP2 and a quantitative measure of language ability in a population-based cohort of European decent (n = 812). No significant associations were found for a panel of 13 SNPs that covered the coding region of FOXP2 and extended into the promoter region. Power analyses indicated we should have been able to detect a QTL variance of 0.02 for an associated allele with MAF of 0.2 or greater with 80% power. This suggests that, if a common variant associated with language ability in this gene does exist, it is likely of small effect. Our findings lead us to conclude that while genetic variants in FOXP2 may be significant for rare forms of language impairment, they do not contribute appreciably to individual variation in the normal range as found in the general population.
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Affiliation(s)
- Kathryn L. Mueller
- Hearing, Language and Literacy, Murdoch Childrens Institute, Melbourne, Australia
- Dept. of Communication Sciences and Disorders, The University of Iowa, Iowa City, United States of America
- * E-mail:
| | - Jeffrey C. Murray
- Dept. of Pediatrics, The University of Iowa, Iowa City, United States of America
| | - Jacob J. Michaelson
- Dept. of Psychiatry, The University of Iowa, Iowa City, United States of America
| | | | | | - J. Bruce Tomblin
- Dept. of Communication Sciences and Disorders, The University of Iowa, Iowa City, United States of America
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47
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Kornilov SA, Rakhlin N, Koposov R, Lee M, Yrigollen C, Caglayan AO, Magnuson JS, Mane S, Chang JT, Grigorenko EL. Genome-Wide Association and Exome Sequencing Study of Language Disorder in an Isolated Population. Pediatrics 2016; 137:peds.2015-2469. [PMID: 27016271 PMCID: PMC4811310 DOI: 10.1542/peds.2015-2469] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/26/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND AND OBJECTIVE Developmental language disorder (DLD) is a highly prevalent neurodevelopmental disorder associated with negative outcomes in different domains; the etiology of DLD is unknown. To investigate the genetic underpinnings of DLD, we performed genome-wide association and whole exome sequencing studies in a geographically isolated population with a substantially elevated prevalence of the disorder (ie, the AZ sample). METHODS DNA samples were collected from 359 individuals for the genome-wide association study and from 12 severely affected individuals for whole exome sequencing. Multifaceted phenotypes, representing major domains of expressive language functioning, were derived from collected speech samples. RESULTS Gene-based analyses revealed a significant association between SETBP1 and complexity of linguistic output (P = 5.47 × 10(-7)). The analysis of exome variants revealed coding sequence variants in 14 genes, most of which play a role in neural development. Targeted enrichment analysis implicated myocyte enhancer factor-2 (MEF2)-regulated genes in DLD in the AZ population. The main findings were successfully replicated in an independent cohort of children at risk for related disorders (n = 372). CONCLUSIONS MEF2-regulated pathways were identified as potential candidate pathways in the etiology of DLD. Several genes (including the candidate SETBP1 and other MEF2-related genes) seem to jointly influence certain, but not all, facets of the DLD phenotype. Even when genetic and environmental diversity is reduced, DLD is best conceptualized as etiologically complex. Future research should establish whether the signals detected in the AZ population can be replicated in other samples and languages and provide further characterization of the identified pathway.
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Affiliation(s)
- Sergey A. Kornilov
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Department of Psychology, University of Connecticut, Storrs, Connecticut;,Haskins Laboratories, New Haven, Connecticut;,Department of Psychology, Moscow State University, Moscow, Russia;,Department of Psychology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Natalia Rakhlin
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Department of Communication Sciences and Disorders, Wayne State University, Detroit, Michigan
| | - Roman Koposov
- Regional Centre for Child and Youth Mental Health and Child Welfare, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maria Lee
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut
| | - Carolyn Yrigollen
- The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ahmet Okay Caglayan
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Department of Medical Genetics, Istanbul Bilim University, Istanbul, Turkey; and
| | - James S. Magnuson
- Department of Psychology, University of Connecticut, Storrs, Connecticut;,Haskins Laboratories, New Haven, Connecticut
| | - Shrikant Mane
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut
| | - Joseph T. Chang
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut
| | - Elena L. Grigorenko
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Haskins Laboratories, New Haven, Connecticut;,Department of Psychology, Saint Petersburg State University, Saint Petersburg, Russia;,Moscow State University for Psychology and Education, Moscow, Russia
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48
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Evans PD, Mueller KL, Gamazon ER, Cox NJ, Tomblin JB. A genome-wide sib-pair scan for quantitative language traits reveals linkage to chromosomes 10 and 13. Genes Brain Behav 2016; 14:387-97. [PMID: 25997078 DOI: 10.1111/gbb.12223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 05/06/2015] [Accepted: 05/06/2015] [Indexed: 02/03/2023]
Abstract
Although there is considerable evidence that individual differences in language development are highly heritable, there have been few genome-wide scans to locate genes associated with the trait. Previous analyses of language impairment have yielded replicable evidence for linkage to regions on chromosomes 16q, 19q, 13q (within lab) and at 13q (between labs). Here we report the first linkage study to screen the continuum of language ability, from normal to disordered, as found in the general population. 383 children from 147 sib-ships (214 sib-pairs) were genotyped on the Illumina(®) Linkage IVb Marker Panel using three composite language-related phenotypes and a measure of phonological memory (PM). Two regions (10q23.33; 13q33.3) yielded genome-wide significant peaks for linkage with PM. A peak suggestive of linkage was also found at 17q12 for the overall language composite. This study presents two novel genetic loci for the study of language development and disorders, but fails to replicate findings by previous groups. Possible reasons for this are discussed.
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Affiliation(s)
- P D Evans
- Department of Medicine, The University of Chicago, IL, USA
| | - K L Mueller
- Murdoch Childrens Research Institute, Melbourne, Australia.,Department of Communication Sciences and Disorders, The University of Iowa, IA, USA
| | - E R Gamazon
- Department of Medicine, The University of Chicago, IL, USA.,Present address: Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - N J Cox
- Department of Medicine, The University of Chicago, IL, USA.,Department of Communication Sciences and Disorders, The University of Iowa, IA, USA.,Present address: Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - J B Tomblin
- Department of Communication Sciences and Disorders, The University of Iowa, IA, USA
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49
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Massinen S, Wang J, Laivuori K, Bieder A, Tapia Paez I, Jiao H, Kere J. Genomic sequencing of a dyslexia susceptibility haplotype encompassing ROBO1. J Neurodev Disord 2016; 8:4. [PMID: 26877820 PMCID: PMC4751651 DOI: 10.1186/s11689-016-9136-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/17/2016] [Indexed: 12/19/2022] Open
Abstract
Background The DYX5 locus for developmental dyslexia was mapped to chromosome 3 by linkage study of a large Finnish family, and later, roundabout guidance receptor 1 (ROBO1) was implicated as a candidate gene at DYX5 with suppressed expression from the segregating rare haplotype. A functional magnetoencephalographic study of several family members revealed abnormal auditory processing of interaural interaction, supporting a defect in midline crossing of auditory pathways. In the current study, we have characterized genetic variation in the broad ROBO1 gene region in the DYX5-linked family, aiming to identify variants that would increase our understanding of the altered expression of ROBO1. Methods We have used a whole genome sequencing strategy on a pooled sample of 19 individuals in combination with two individually sequenced genomes. The discovered genetic variants were annotated and filtered. Subsequently, the most interesting variants were functionally tested using relevant methods, including electrophoretic mobility shift assay (EMSA), luciferase assay, and gene knockdown by lentiviral small hairpin RNA (shRNA) in lymphoblasts. Results We found one novel intronic single nucleotide variant (SNV) and three novel intergenic SNVs in the broad region of ROBO1 that were specific to the dyslexia susceptibility haplotype. Functional testing by EMSA did not support the binding of transcription factors to three of the SNVs, but one of the SNVs was bound by the LIM homeobox 2 (LHX2) protein, with increased binding affinity for the non-reference allele. Knockdown of LHX2 in lymphoblast cell lines extracted from subjects from the DYX5-linked family showed decreasing expression of ROBO1, supporting the idea that LHX2 regulates ROBO1 also in human. Conclusions The discovered variants may explain the segregation of dyslexia in this family, but the effect appears subtle in the experimental settings. Their impact on the developing human brain remains suggestive based on the association and subtle experimental support. Electronic supplementary material The online version of this article (doi:10.1186/s11689-016-9136-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Satu Massinen
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland ; Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland
| | - Jingwen Wang
- Department of Biosciences and Nutrition, and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Krista Laivuori
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland ; Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland
| | - Andrea Bieder
- Department of Biosciences and Nutrition, and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Isabel Tapia Paez
- Department of Biosciences and Nutrition, and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Hong Jiao
- Department of Biosciences and Nutrition, and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland ; Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland ; Department of Biosciences and Nutrition, and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
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50
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Lee JC, Mueller KL, Tomblin JB. Examining Procedural Learning and Corticostriatal Pathways for Individual Differences in Language: Testing Endophenotypes of DRD2/ANKK1. Lang Cogn Neurosci 2016; 31:1098-1114. [PMID: 31768398 PMCID: PMC6876848 DOI: 10.1080/23273798.2015.1089359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The aim of the study was to explore whether genetic variation in the dopaminergic system is associated with procedural learning and the corticostriatal pathways in individuals with developmental language impairment (DLI). We viewed these two systems as endophenotypes and hypothesized that they would be more sensitive indicators of genetic effects than the language phenotype itself. Thus, we genotyped two SNPs in the DRD2/ANKK1 gene complex, and tested for their associations to the phenotype of DLI and the two endophenotypes. Results showed that individuals with DLI revealed poor procedural learning abilities and abnormal structures of the basal ganglia. Genetic variation in DRD2/ANKK1 was associated with procedural learning abilities and with microstructural differences of the caudate nucleus. The association of the language phenotype with these DRD2/ANKK1 polymorphisms was not significant, but the phenotype was significantly associated with the two endophenotypes. We suggest that procedural learning and the corticostriatal pathways could be used as effective endophenotypes to aid molecular genetic studies searching for genes predisposing to DLI.
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Affiliation(s)
- Joanna C. Lee
- Department of Communication Sciences and Disorders, University of Iowa, Iowa City, IA, USA
| | - Kathryn L. Mueller
- Department of Communication Sciences and Disorders, University of Iowa, Iowa City, IA, USA
| | - J. Bruce Tomblin
- Department of Communication Sciences and Disorders, University of Iowa, Iowa City, IA, USA
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